LMU BioDB 2013 - User contributions [en]

Team H(oo)KD Final Project Deliverables

2013-12-14T00:38:57Z

Dwilliams: /* Deliverables */ Fixed error

{{Team H(oo)KD}}

==Deliverables==

*Gene database for ''Chlamydia trachomatis'' A/HAR-13 (.gdb): [[Media:Ct-Std External 20131121.gdb|Ct-Std_External_20131121.gdb]]
*ReadMe file including the gene database schema:[[Media:ReadMe Ct-Std External 20131122.pdf|ReadMe_Ct-Std_External_20131122.pdf]]
*Gene database testing report: [[Media:Ct External 20131121 Gene Database Testing Report.pdf|Ct_External_20131121_Gene_Database_Testing_Report.pdf]]
*Processed and analyzed DNA microarray dataset (.xls):[[Media:Final Excel Sheet Used for Project.xls | processed and analyzed DNA microarray dataset]]
*GenMAPP Expression Dataset file (.gex):
:*For data collected in absence of rifampicin: [[Media: For GenMAPP Chlamydia V4 20131205 KS.gex|For_GenMAPP_Absence_of_Rifampicin.gex]]
:*For data collected in presence of rifampicin: [[Media:For GenMAPP Chlamydia V4 20131212 KS Presence of Rifampicin.gex|For_GenMAPP Chlamydia_V4_20131212_KS_Presence_of_Rifampicin.gex]]
*Filtered MAPPFinder Results (.xls):
*[[Media: EB to RB No Rif 20131207 KS DW-Criterion0-GO.xls|EB to RB No Rif Increased]]
*[[Media: EB to RB No Rif 20131207 KS DW-Criterion1-GO.xls|EB to RB No Rif decreased]]
*[[Media: MAPPFinder Results EB to RB Rifampicin 20131212-Criterion0-GO (1).xls ‎| EB to RB Rif Increased]]
*[[Media:EB to RB No Rif 20131207 KS DW-Criterion1-GO.xls|EB to RB No Rif decreased]]
*Sample MAPP file of a relevant biological pathway for your species (.mapp):[[Media:EBtoRB_Rifampicin_Cellular_Carbohydrate_Metabolic_Process.mapp]]
:*Picture of the MAPP (.jpeg):[[Media:EBtoRB Rifampicin Cellular Carbohydrate Metabolic Process.jpg]]
*Group Report (.pdf): [[Media:Report for Final Project HDDWKS 20131213.pdf|Report_for_Final_Project_HDDWKS_20131213.pdf]]
*PowerPoint presentation (given on Thursday, December 12): [[Media:Transcriptional_Analysis_of_the_Developmental_Stages_of_Chlamydia_trachomatis_A_HAR-13_HDKSDW_20131212.pdf|Transcriptional_Analysis_of_the_Developmental_Stages_of_Chlamydia_trachomatis_A_HAR-13_HDKSDW_20131212.pdf]]

Team H(oo)KD Final Project Deliverables

2013-12-14T00:38:34Z

Dwilliams: /* Deliverables */ added dna microarray dataset

{{Team H(oo)KD}}

==Deliverables==

*Gene database for ''Chlamydia trachomatis'' A/HAR-13 (.gdb): [[Media:Ct-Std External 20131121.gdb|Ct-Std_External_20131121.gdb]]
*ReadMe file including the gene database schema:[[Media:ReadMe Ct-Std External 20131122.pdf|ReadMe_Ct-Std_External_20131122.pdf]]
*Gene database testing report: [[Media:Ct External 20131121 Gene Database Testing Report.pdf|Ct_External_20131121_Gene_Database_Testing_Report.pdf]]
*Processed and analyzed DNA microarray dataset (.xls):[[Media:Final Excel Sheet Used for Project.xls | rocessed and analyzed DNA microarray dataset]]
*GenMAPP Expression Dataset file (.gex):
:*For data collected in absence of rifampicin: [[Media: For GenMAPP Chlamydia V4 20131205 KS.gex|For_GenMAPP_Absence_of_Rifampicin.gex]]
:*For data collected in presence of rifampicin: [[Media:For GenMAPP Chlamydia V4 20131212 KS Presence of Rifampicin.gex|For_GenMAPP Chlamydia_V4_20131212_KS_Presence_of_Rifampicin.gex]]
*Filtered MAPPFinder Results (.xls):
*[[Media: EB to RB No Rif 20131207 KS DW-Criterion0-GO.xls|EB to RB No Rif Increased]]
*[[Media: EB to RB No Rif 20131207 KS DW-Criterion1-GO.xls|EB to RB No Rif decreased]]
*[[Media: MAPPFinder Results EB to RB Rifampicin 20131212-Criterion0-GO (1).xls ‎| EB to RB Rif Increased]]
*[[Media:EB to RB No Rif 20131207 KS DW-Criterion1-GO.xls|EB to RB No Rif decreased]]
*Sample MAPP file of a relevant biological pathway for your species (.mapp):[[Media:EBtoRB_Rifampicin_Cellular_Carbohydrate_Metabolic_Process.mapp]]
:*Picture of the MAPP (.jpeg):[[Media:EBtoRB Rifampicin Cellular Carbohydrate Metabolic Process.jpg]]
*Group Report (.pdf): [[Media:Report for Final Project HDDWKS 20131213.pdf|Report_for_Final_Project_HDDWKS_20131213.pdf]]
*PowerPoint presentation (given on Thursday, December 12): [[Media:Transcriptional_Analysis_of_the_Developmental_Stages_of_Chlamydia_trachomatis_A_HAR-13_HDKSDW_20131212.pdf|Transcriptional_Analysis_of_the_Developmental_Stages_of_Chlamydia_trachomatis_A_HAR-13_HDKSDW_20131212.pdf]]

Team H(oo)KD Final Project Deliverables

2013-12-14T00:32:23Z

Dwilliams: /* Deliverables */ added jpeg

{{Team H(oo)KD}}

==Deliverables==

*Gene database for ''Chlamydia trachomatis'' A/HAR-13 (.gdb): [[Media:Ct-Std External 20131121.gdb|Ct-Std_External_20131121.gdb]]
*ReadMe file including the gene database schema:[[Media:ReadMe Ct-Std External 20131122.pdf|ReadMe_Ct-Std_External_20131122.pdf]]
*Gene database testing report: [[Media:Ct External 20131121 Gene Database Testing Report.pdf|Ct_External_20131121_Gene_Database_Testing_Report.pdf]]
*Processed and analyzed DNA microarray dataset (.xls):
*GenMAPP Expression Dataset file (.gex):
:*For data collected in absence of rifampicin: [[Media: For GenMAPP Chlamydia V4 20131205 KS.gex|For_GenMAPP_Absence_of_Rifampicin.gex]]
:*For data collected in presence of rifampicin: [[Media:For GenMAPP Chlamydia V4 20131212 KS Presence of Rifampicin.gex|For_GenMAPP Chlamydia_V4_20131212_KS_Presence_of_Rifampicin.gex]]
*Filtered MAPPFinder Results (.xls):
*[[Media: EB to RB No Rif 20131207 KS DW-Criterion0-GO.xls|EB to RB No Rif Increased]]
*[[Media: EB to RB No Rif 20131207 KS DW-Criterion1-GO.xls|EB to RB No Rif decreased]]
*[[Media: MAPPFinder Results EB to RB Rifampicin 20131212-Criterion0-GO (1).xls ‎| EB to RB Rif Increased]]
*[[Media:EB to RB No Rif 20131207 KS DW-Criterion1-GO.xls|EB to RB No Rif decreased]]
*Sample MAPP file of a relevant biological pathway for your species (.mapp):[[Media:EBtoRB_Rifampicin_Cellular_Carbohydrate_Metabolic_Process.mapp]]
:*Picture of the MAPP (.jpeg):[[Media:EBtoRB Rifampicin Cellular Carbohydrate Metabolic Process.jpg]]
*Group Report (.pdf):
*PowerPoint presentation (given on Thursday, December 12):

File:EBtoRB Rifampicin Cellular Carbohydrate Metabolic Process.jpg

2013-12-14T00:31:52Z

Dwilliams: Cellular Carbohydrate Metabolic Process.jpeg

Cellular Carbohydrate Metabolic Process.jpeg

Team H(oo)KD Final Project Deliverables

2013-12-14T00:30:43Z

Dwilliams: /* Deliverables */ added mapp

{{Team H(oo)KD}}

==Deliverables==

*Gene database for ''Chlamydia trachomatis'' A/HAR-13 (.gdb): [[Media:Ct-Std External 20131121.gdb|Ct-Std_External_20131121.gdb]]
*ReadMe file including the gene database schema:[[Media:ReadMe Ct-Std External 20131122.pdf|ReadMe_Ct-Std_External_20131122.pdf]]
*Gene database testing report: [[Media:Ct External 20131121 Gene Database Testing Report.pdf|Ct_External_20131121_Gene_Database_Testing_Report.pdf]]
*Processed and analyzed DNA microarray dataset (.xls):
*GenMAPP Expression Dataset file (.gex):
:*For data collected in absence of rifampicin: [[Media: For GenMAPP Chlamydia V4 20131205 KS.gex|For_GenMAPP_Absence_of_Rifampicin.gex]]
:*For data collected in presence of rifampicin: [[Media:For GenMAPP Chlamydia V4 20131212 KS Presence of Rifampicin.gex|For_GenMAPP Chlamydia_V4_20131212_KS_Presence_of_Rifampicin.gex]]
*Filtered MAPPFinder Results (.xls):
*[[Media: EB to RB No Rif 20131207 KS DW-Criterion0-GO.xls|EB to RB No Rif Increased]]
*[[Media: EB to RB No Rif 20131207 KS DW-Criterion1-GO.xls|EB to RB No Rif decreased]]
*[[Media: MAPPFinder Results EB to RB Rifampicin 20131212-Criterion0-GO (1).xls ‎| EB to RB Rif Increased]]
*[[Media:EB to RB No Rif 20131207 KS DW-Criterion1-GO.xls|EB to RB No Rif decreased]]
*Sample MAPP file of a relevant biological pathway for your species (.mapp):[[Media:EBtoRB_Rifampicin_Cellular_Carbohydrate_Metabolic_Process.mapp]]
:*Picture of the MAPP (.jpeg):
*Group Report (.pdf):
*PowerPoint presentation (given on Thursday, December 12):

File:EBtoRB Rifampicin Cellular Carbohydrate Metabolic Process.mapp

2013-12-14T00:30:14Z

Dwilliams: Cellular Carbohydrate Metabolic Process.mapp file

Cellular Carbohydrate Metabolic Process.mapp file

Team H(oo)KD Final Project Deliverables

2013-12-14T00:27:54Z

Dwilliams: /* Deliverables */ Added filtered mappfinder results

{{Team H(oo)KD}}

==Deliverables==

*Gene database for ''Chlamydia trachomatis'' A/HAR-13 (.gdb): [[Media:Ct-Std External 20131121.gdb|Ct-Std_External_20131121.gdb]]
*ReadMe file including the gene database schema:[[Media:ReadMe Ct-Std External 20131122.pdf|ReadMe_Ct-Std_External_20131122.pdf]]
*Gene database testing report: [[Media:Ct External 20131121 Gene Database Testing Report.pdf|Ct_External_20131121_Gene_Database_Testing_Report.pdf]]
*Processed and analyzed DNA microarray dataset (.xls):
*GenMAPP Expression Dataset file (.gex):
:*For data collected in absence of rifampicin: [[Media: For GenMAPP Chlamydia V4 20131205 KS.gex|For_GenMAPP_Absence_of_Rifampicin.gex]]
:*For data collected in presence of rifampicin: [[Media:For GenMAPP Chlamydia V4 20131212 KS Presence of Rifampicin.gex|For_GenMAPP Chlamydia_V4_20131212_KS_Presence_of_Rifampicin.gex]]
*Filtered MAPPFinder Results (.xls):
*[[Media: EB to RB No Rif 20131207 KS DW-Criterion0-GO.xls|EB to RB No Rif Increased]]
*[[Media: EB to RB No Rif 20131207 KS DW-Criterion1-GO.xls|EB to RB No Rif decreased]]
*[[Media: MAPPFinder Results EB to RB Rifampicin 20131212-Criterion0-GO (1).xls ‎| EB to RB Rif Increased]]
*[[Media:EB to RB No Rif 20131207 KS DW-Criterion1-GO.xls|EB to RB No Rif decreased]]
*Sample MAPP file of a relevant biological pathway for your species (.mapp):
:*Picture of the MAPP (.jpeg):
*Group Report (.pdf):
*PowerPoint presentation (given on Thursday, December 12):

File:MAPPFinder Results EB to RB Rifampicin 20131212-Criterion1-GO (1).xls

2013-12-14T00:24:54Z

Dwilliams: EB to RB Rif Decreased

EB to RB Rif Decreased

File:MAPPFinder Results EB to RB Rifampicin 20131212-Criterion0-GO (1).xls

2013-12-14T00:24:23Z

Dwilliams: EB to RB Rif Increased

EB to RB Rif Increased

File:EB to RB No Rif 20131207 KS DW-Criterion1-GO.xls

2013-12-14T00:22:36Z

Dwilliams: EB to RB No Rif decreased

EB to RB No Rif decreased

File:EB to RB No Rif 20131207 KS DW-Criterion0-GO.xls

2013-12-14T00:22:01Z

Dwilliams: EB to RB No Rif Increased

EB to RB No Rif Increased

Team H(oo)KD Final Project Deliverables

2013-12-14T00:16:43Z

Dwilliams: /* Deliverables */ added fenmapp color set

{{Team H(oo)KD}}

==Deliverables==

*Gene database for ''Chlamydia trachomatis'' A/HAR-13 (.gdb): [[Media:Ct-Std External 20131121.gdb|Ct-Std_External_20131121.gdb]]
*ReadMe file including the gene database schema:
*Gene database testing report: [[Media:Ct External 20131121 Gene Database Testing Report.pdf|Ct_External_20131121_Gene_Database_Testing_Report.pdf]]
*Processed and analyzed DNA microarray dataset (.xls):
*GenMAPP Expression Dataset file (.gex):
:*For data collected in absence of rifampicin: [[Media: For GenMAPP Chlamydia V4 20131205 KS.gex|For GenMAPP absence of Rifampicin]]
:*For data collected in presence of rifampicin: [[Media:For GenMAPP Chlamydia V4 20131212 KS Presence of Rifampicin.gex|For_GenMAPP Chlamydia_V4_20131212_KS_Presence_of_Rifampicin.gex]]
*Filtered MAPPFinder Results (.xls):
*Sample MAPP file of a relevant biological pathway for your species (.mapp):
:*Picture of the MAPP (.jpeg):
*Group Report (.pdf):
*PowerPoint presentation (given on Thursday, December 12):

Chlamydia trachomatis

2013-12-13T23:36:47Z

Dwilliams: /* Important Files */ Formatting

{{Team_H(oo)KD}}

==Deadlines and Intermediate Milestones==

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 8em; background: #ddd" | Monday
! style="width: 8em; background: #ddd" | Tuesday
! style="width: 8em; background: #ddd" | Wednesday
! style="width: 8em; background: #ddd" | Thursday
! style="width: 8em; background: #ddd" | Friday
|-
| style="vertical-align: top" | 11/11
| style="vertical-align: top" | 11/12
| style="vertical-align: top" | 11/13
| style="vertical-align: top" | 11/14
*Run an export/import of gene database cycle '''KS/HD'''
*Create species profile '''KS'''
*Obtain and format raw microarray data '''DW'''
| style="vertical-align: top" | 11/15
*Rerun export/import of gene database cycle '''KS'''
|-
| style="vertical-align: top; background: #eee" | 11/18
| style="vertical-align: top; background: #eee" | 11/19
*Vet the gene database exported last week '''KS/HD/DW'''
*Format the raw microarray data '''DW'''
| style="vertical-align: top; background: #eee" | 11/20
| style="vertical-align: top; background: #eee" | 11/21
*Perform microarray statistical analysis '''DW'''
*Work on custom species profile '''KS/HD'''
| style="vertical-align: top; background: #eee" | 11/22
|-
| style="vertical-align: top" | 11/25
| style="vertical-align: top" | 11/26
*Build and commit species profile '''KS'''
*Customize Tally Engine '''KS/HD'''
*Perform GenMAPP and MAPPFinder Analysis '''DW'''
| style="vertical-align: top" | 11/27
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/28
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/29
'''THANKSGIVING BREAK'''
|-
| style="vertical-align: top; background: #eee" | 12/02
| style="vertical-align: top; background: #eee" | 12/03
*Run GenMAPP and MAPPFinder '''DW'''
*Customize the Tally Engine for ''C. trachomatis'' '''DW'''
| style="vertical-align: top; background: #eee" | 12/04
*Run GenMAPP and MAPPFinder again if necessary '''DW'''
| style="vertical-align: top; background: #eee" | 12/05
*Begin working on the relational database schema '''HD'''
*Commit the changes to gmbuilder '''KS'''
| style="vertical-align: top; background: #eee" | 12/06
|-
| style="vertical-align: top; background: #eee" | 12/09
*Write the paper '''HD/KS/DW'''
*Work on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/10
*Write the paper '''HD/KS/DW'''
*Work on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/11
*Finish the presentation '''HD/KS/DW'''
*Practice the final presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/12
*'''Final Presentation'''
*Proofread the final paper '''HD/KS/DW'''
*Make sure all the deliverables are raedy '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/13
|}

==Deliverable and Final Paper Assignments==

===Deliverables===

*GenMAPP Gene Database for assigned species (.gdb) '''Katrina'''
*ReadMe file to accompany the Gene Database (.pdf)
:*Include Gene Database Schema diagram in ReadMe '''Hilda'''
*Gene Database Testing Report for final submitted Gene Database (print from wiki to .pdf file) '''Katrina'''
*Processed and analyzed DNA microarray dataset (.xls) '''Dillon'''
*GenMAPP Expression Dataset file (.gex) '''Dillon'''
*Filtered MAPPFinder Results (.xls) '''Dillon'''
*Sample MAPP file of a relevant biological pathway for your species (.mapp) '''Dillon'''

===Final Paper===

#Introduction '''Hilda'''
#Methods
#*Download the UniProt XML proteome set and GOA (GO association) files for your species. '''Katrina'''
#*Download GO terms from in the OBO-XML format. '''Katrina'''
#*Create the GenMAPP Builder tables in PostgreSQL. '''Katrina'''
#*Load files into PostgreSQL database via GenMAPP Builder. '''Katrina'''
#*Export into a GenMAPP Gene Database. '''Katrina'''
#*Inspect/vet/validate Gene Database. '''Katrina'''
#*Prepare microarray data (organize, normalize, perform statistical analysis) '''Dillon'''
#*Run GenMAPP and MAPPFinder using the Gene Database. '''Dillon'''
#Results
#*Gene Database Schema '''Hilda'''
#*Gene Database Testing Report on final version of Gene Database '''Katrina'''
#*Report on quantity and identity of gene IDs that did not make it into the database '''Hilda'''
#*Report on what changes need to be made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs '''Katrina'''
#*Report results of the DNA microarray statistical analysis '''Dillon'''
#*Table of MAPPFinder results (from .xls) and MAPP of a pathway '''Dillon'''
#Discussion
#*How well did the GenMAPP Builder process work for your species? '''Katrina'''
#*Discuss the statistical analysis and MAPPFinder results for your microarray dataset. '''Dillon'''

==Annotated Bibliography of Genomics Papers for ''C. trachomatis''==

===Whole genome sequencing of ''C. trachomatis''===

#Journal article describing results of whole genome sequencing:
#*Database: PubMed
#*Search Terms: Chlamydia trachomatis [MeSH Term] AND genome [Title]
#*There were 29 results. Many of the articles that appear using the above search terms have to do with performing whole-genome analysis of ''C. trachomatis'' to look at genetic polymorphisms in the bacterium and molecular and genetic characteristics that are observed when the bacterium infects a host.
#*Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R., Zhao, Q., Koonin, E. V., Davis, R.W. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. ''Science'' '''282''': 754-759. 10.1126/science.282.5389.754.
#*The article can be viewed as an [http://www.sciencemag.org/content/282/5389/754.long HTML].
#*The article can be viewed as a [[Media: Science-1998-Stephens-754-9.pdf | PDF]].
#*This article includes [http://www.sciencemag.org/site/feature/data/982604.xhtml Supplementary Material].
#Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
#*How many results did you get?: 872
#*Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?: Based on the titles and abstracts found in the results, it seems that research has been primarily in the direction of understanding how the disease functions and assessing the severity of the disease (and how to cure it).

===Microarray articles===
The EBI ArrayExpress database was used to locate each of the four following microarray articles. The search terms used were Chlamydia trachomatis under 'By organism' while the rest of the drop down menus were not altered.

The following articles appear in order of preference:

#Omsland, A., Sager, J., Nair, V., Sturdevant, D.E., Hackstadt, T. (2012) [http://www.pnas.org/content/109/48/19781.full Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]. ''PNAS'' '''109''': 19781-19785. doi: 10.1073/pnas.1212831109.
#*[[Media: PNAS-2012-Omsland-19781-5.pdf|PDF Version of Paper]]
#*[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data]
#*Chlamydiae undergo a biphasic developmental cycle characterized by an infectious cell type known as either an elementary body (EB) and an intracellular replicative form called a reticulate body (RB). Chlamydia was incubated under microaerobic conditions to test the differences in preferred energy source between EB's and RB's.
#*There weren't necessarily a "treatment" group and a "control" group. Referencing figure 4, it can be inferred that EB would be considered the "treatment" group because of the way that the ratio was set up, being EB to RB. In this way the RB would be the "control" group as they are looking at the EB population relative to the RB population.
#*4 Biological Replicates were performed for the control and treatment; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates...".


==Journal Club Presentation on ''C. trachomatis'' Genome Sequencing Paper==

[[Media:Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf|Here]] is the PDF version of the presentation given on November 12, 2013 on the Stephens ''et al.'' (1998) paper.


==Important Files==

*[[Media: Go_daily-termdb_v2_HD_20131107.obo-xml.gz|Go_daily-termdb_v2_HD_20131107.obo-xml.gz]]
:GO OBO-XML file for ''C. trachomatis'' serovar A.
*[[Media: Uniprot XML C.trachomatis serovar A KS 20131114.xml|Uniprot XML C.trachomatis serovar A KS 20131114.xml]]
:UniProt XML file for ''C. trachomatis'' serovar A.
*[[Media: 22183.C trachomatis A KS 20131114.goa|22183.C trachomatis A KS 20131114.goa]]
:GOA file for ''C. trachomatis'' serovar A.
*[[Media: Ct-Std v1 KS 20131119.gdb|Ct-Std v1 KS 20131119.gdb]]
:First iteration of the export/import gene database cycle.
*[[Media: Ct-Std KS 20131121.gdb|Ct-Std KS 20131121.gdb]]
:Updated gene database.
*[[Media: Ct-Std v2 KS 20131121.gdb|Ct-Std v2 KS 20131121.gdb]]
:New gene database created with the new version of gmbuilder built on 11/21/2013 using the custom species profile for ''C. trachomatis.''

'''Array Express Article Raw Files'''

*[[Media:Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt|Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt]]
:Microarray raw ADF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt]]
:Microarray raw IDF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip]]
:Microarray raw processed zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip]]
:Microarray raw zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt]]
:Microarray SDRF text file for ''C. trachomatis''.
*[[Media:Sdrf information excel.xls|Sdrf information excel.xls]]
:sdrf information in excel spreadsheet format.

'''Excel Master Spreadsheet File Versions (Containing the Formatted Raw Data)'''

*[[Media:Master Spreadsheet.xls|master spreadsheet work in progress]]
:Initial Microarray raw data formatted and opened in Microsoft Excel.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls]]
:Sample C. trachomatis microarray data that was used to run GenMAPP with the latest ''C. trachomatis'' database.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt]]
:Tab-delimited version of the file above.
*[[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]]
:Microarray data with identified Gene ID's and Log base data.
*[[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls | Master_Spreadsheet_Chlamydia_20131125_KD.xls]]
:version edited during office hours by Dr. Dahlquist to demonstrate statistics
*[[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls]]
:finished version of version edited during office hours by Dr. Dahlquist to demonstrate statistics -- finished by Dillon Williams
*[[Media: Copy of Master Spreadsheet Chlamydia V2 20131203 HD.xls]]
:Microarray data with separated IDs CTA_#### from _RRMH#####_...
*[[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]]
:Excel Speadsheet with data formatted for GenMAPP (Version run in GenMAPP).

'''For GenMAPP Files'''
*[[Media: Ctrachomatis EbtoRb ATP metabolic process.mapp]]
: EB to RB ATP Metabolic Process Mapp file.
*[[Media: Ctrachomatis EbtoRB glucose catabolic process 20131204 DW.mapp]]
: EB to RB glucose catabolic process map.
*[[Media: CTrachomatis EBtoRB Rifampicin 20131204 DW-Criterion1-GO.txt]]
: EB to RB Rifampicin go.txt file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.gex]]
: For_GenMAPP .gex file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.gmf]]
: For GenMAPP .gmf file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.zip]]
: Access file created with .gex file.
*[[Media: For GenMAPP Chlamydia V4 20131205 KS.gex]]
:Color set created in GenMAPP for EB to RB no rifampicin and increased/decreased logFC criteria

'''MAPPFinder Files'''
*[[Media:EB to RB No Rif V2-Criterion0-GO.txt]]
:Increased
*[[Media: EB to RB No Rif V2-Criterion1-GO.txt]]
:Deceased
*[[Media: For GenMAPP Chlamydia V4 20131205 KS.gmf]]
: File created by MAPPFinder after creating the latest color set.

'''Final Excel Spreadsheet Containing Everything from GenMAPP and MAPPFinder'''
*[[Media: Final Excel Sheet Used for Project.xls]]
:Final excel sheet used for project. Includes all raw data, all EB to RB ratios in the presence and absence of rifampicin, statistical analysis of that data, for GenMAPP data, and all charts and tables used for GO terms and summaries of data

==Wiki Formatting==

Template: [[Template:Team_H(oo)KD]]

[[Category: Group Projects]]
[[Category: Team H(oo)KD]]

Chlamydia trachomatis

2013-12-13T23:36:03Z

Dwilliams: /* Important Files */ Added file

{{Team_H(oo)KD}}

==Deadlines and Intermediate Milestones==

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 8em; background: #ddd" | Monday
! style="width: 8em; background: #ddd" | Tuesday
! style="width: 8em; background: #ddd" | Wednesday
! style="width: 8em; background: #ddd" | Thursday
! style="width: 8em; background: #ddd" | Friday
|-
| style="vertical-align: top" | 11/11
| style="vertical-align: top" | 11/12
| style="vertical-align: top" | 11/13
| style="vertical-align: top" | 11/14
*Run an export/import of gene database cycle '''KS/HD'''
*Create species profile '''KS'''
*Obtain and format raw microarray data '''DW'''
| style="vertical-align: top" | 11/15
*Rerun export/import of gene database cycle '''KS'''
|-
| style="vertical-align: top; background: #eee" | 11/18
| style="vertical-align: top; background: #eee" | 11/19
*Vet the gene database exported last week '''KS/HD/DW'''
*Format the raw microarray data '''DW'''
| style="vertical-align: top; background: #eee" | 11/20
| style="vertical-align: top; background: #eee" | 11/21
*Perform microarray statistical analysis '''DW'''
*Work on custom species profile '''KS/HD'''
| style="vertical-align: top; background: #eee" | 11/22
|-
| style="vertical-align: top" | 11/25
| style="vertical-align: top" | 11/26
*Build and commit species profile '''KS'''
*Customize Tally Engine '''KS/HD'''
*Perform GenMAPP and MAPPFinder Analysis '''DW'''
| style="vertical-align: top" | 11/27
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/28
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/29
'''THANKSGIVING BREAK'''
|-
| style="vertical-align: top; background: #eee" | 12/02
| style="vertical-align: top; background: #eee" | 12/03
*Run GenMAPP and MAPPFinder '''DW'''
*Customize the Tally Engine for ''C. trachomatis'' '''DW'''
| style="vertical-align: top; background: #eee" | 12/04
*Run GenMAPP and MAPPFinder again if necessary '''DW'''
| style="vertical-align: top; background: #eee" | 12/05
*Begin working on the relational database schema '''HD'''
*Commit the changes to gmbuilder '''KS'''
| style="vertical-align: top; background: #eee" | 12/06
|-
| style="vertical-align: top; background: #eee" | 12/09
*Write the paper '''HD/KS/DW'''
*Work on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/10
*Write the paper '''HD/KS/DW'''
*Work on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/11
*Finish the presentation '''HD/KS/DW'''
*Practice the final presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/12
*'''Final Presentation'''
*Proofread the final paper '''HD/KS/DW'''
*Make sure all the deliverables are raedy '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/13
|}

==Deliverable and Final Paper Assignments==

===Deliverables===

*GenMAPP Gene Database for assigned species (.gdb) '''Katrina'''
*ReadMe file to accompany the Gene Database (.pdf)
:*Include Gene Database Schema diagram in ReadMe '''Hilda'''
*Gene Database Testing Report for final submitted Gene Database (print from wiki to .pdf file) '''Katrina'''
*Processed and analyzed DNA microarray dataset (.xls) '''Dillon'''
*GenMAPP Expression Dataset file (.gex) '''Dillon'''
*Filtered MAPPFinder Results (.xls) '''Dillon'''
*Sample MAPP file of a relevant biological pathway for your species (.mapp) '''Dillon'''

===Final Paper===

#Introduction '''Hilda'''
#Methods
#*Download the UniProt XML proteome set and GOA (GO association) files for your species. '''Katrina'''
#*Download GO terms from in the OBO-XML format. '''Katrina'''
#*Create the GenMAPP Builder tables in PostgreSQL. '''Katrina'''
#*Load files into PostgreSQL database via GenMAPP Builder. '''Katrina'''
#*Export into a GenMAPP Gene Database. '''Katrina'''
#*Inspect/vet/validate Gene Database. '''Katrina'''
#*Prepare microarray data (organize, normalize, perform statistical analysis) '''Dillon'''
#*Run GenMAPP and MAPPFinder using the Gene Database. '''Dillon'''
#Results
#*Gene Database Schema '''Hilda'''
#*Gene Database Testing Report on final version of Gene Database '''Katrina'''
#*Report on quantity and identity of gene IDs that did not make it into the database '''Hilda'''
#*Report on what changes need to be made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs '''Katrina'''
#*Report results of the DNA microarray statistical analysis '''Dillon'''
#*Table of MAPPFinder results (from .xls) and MAPP of a pathway '''Dillon'''
#Discussion
#*How well did the GenMAPP Builder process work for your species? '''Katrina'''
#*Discuss the statistical analysis and MAPPFinder results for your microarray dataset. '''Dillon'''

==Annotated Bibliography of Genomics Papers for ''C. trachomatis''==

===Whole genome sequencing of ''C. trachomatis''===

#Journal article describing results of whole genome sequencing:
#*Database: PubMed
#*Search Terms: Chlamydia trachomatis [MeSH Term] AND genome [Title]
#*There were 29 results. Many of the articles that appear using the above search terms have to do with performing whole-genome analysis of ''C. trachomatis'' to look at genetic polymorphisms in the bacterium and molecular and genetic characteristics that are observed when the bacterium infects a host.
#*Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R., Zhao, Q., Koonin, E. V., Davis, R.W. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. ''Science'' '''282''': 754-759. 10.1126/science.282.5389.754.
#*The article can be viewed as an [http://www.sciencemag.org/content/282/5389/754.long HTML].
#*The article can be viewed as a [[Media: Science-1998-Stephens-754-9.pdf | PDF]].
#*This article includes [http://www.sciencemag.org/site/feature/data/982604.xhtml Supplementary Material].
#Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
#*How many results did you get?: 872
#*Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?: Based on the titles and abstracts found in the results, it seems that research has been primarily in the direction of understanding how the disease functions and assessing the severity of the disease (and how to cure it).

===Microarray articles===
The EBI ArrayExpress database was used to locate each of the four following microarray articles. The search terms used were Chlamydia trachomatis under 'By organism' while the rest of the drop down menus were not altered.

The following articles appear in order of preference:

#Omsland, A., Sager, J., Nair, V., Sturdevant, D.E., Hackstadt, T. (2012) [http://www.pnas.org/content/109/48/19781.full Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]. ''PNAS'' '''109''': 19781-19785. doi: 10.1073/pnas.1212831109.
#*[[Media: PNAS-2012-Omsland-19781-5.pdf|PDF Version of Paper]]
#*[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data]
#*Chlamydiae undergo a biphasic developmental cycle characterized by an infectious cell type known as either an elementary body (EB) and an intracellular replicative form called a reticulate body (RB). Chlamydia was incubated under microaerobic conditions to test the differences in preferred energy source between EB's and RB's.
#*There weren't necessarily a "treatment" group and a "control" group. Referencing figure 4, it can be inferred that EB would be considered the "treatment" group because of the way that the ratio was set up, being EB to RB. In this way the RB would be the "control" group as they are looking at the EB population relative to the RB population.
#*4 Biological Replicates were performed for the control and treatment; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates...".


==Journal Club Presentation on ''C. trachomatis'' Genome Sequencing Paper==

[[Media:Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf|Here]] is the PDF version of the presentation given on November 12, 2013 on the Stephens ''et al.'' (1998) paper.


==Important Files==

*[[Media: Go_daily-termdb_v2_HD_20131107.obo-xml.gz|Go_daily-termdb_v2_HD_20131107.obo-xml.gz]]
:GO OBO-XML file for ''C. trachomatis'' serovar A.
*[[Media: Uniprot XML C.trachomatis serovar A KS 20131114.xml|Uniprot XML C.trachomatis serovar A KS 20131114.xml]]
:UniProt XML file for ''C. trachomatis'' serovar A.
*[[Media: 22183.C trachomatis A KS 20131114.goa|22183.C trachomatis A KS 20131114.goa]]
:GOA file for ''C. trachomatis'' serovar A.
*[[Media: Ct-Std v1 KS 20131119.gdb|Ct-Std v1 KS 20131119.gdb]]
:First iteration of the export/import gene database cycle.
*[[Media: Ct-Std KS 20131121.gdb|Ct-Std KS 20131121.gdb]]
:Updated gene database.
*[[Media: Ct-Std v2 KS 20131121.gdb|Ct-Std v2 KS 20131121.gdb]]
:New gene database created with the new version of gmbuilder built on 11/21/2013 using the custom species profile for ''C. trachomatis.''

'''Array Express Article Raw Files'''

*[[Media:Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt|Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt]]
:Microarray raw ADF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt]]
:Microarray raw IDF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip]]
:Microarray raw processed zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip]]
:Microarray raw zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt]]
:Microarray SDRF text file for ''C. trachomatis''.
*[[Media:Sdrf information excel.xls|Sdrf information excel.xls]]
:sdrf information in excel spreadsheet format.

'''Excel Master Spreadsheet File Versions (Containing the Formatted Raw Data)'''

*[[Media:Master Spreadsheet.xls|master spreadsheet work in progress]]
:Initial Microarray raw data formatted and opened in Microsoft Excel.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls]]
:Sample C. trachomatis microarray data that was used to run GenMAPP with the latest ''C. trachomatis'' database.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt]]
:Tab-delimited version of the file above.
*[[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]]
:Microarray data with identified Gene ID's and Log base data.
*[[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls | Master_Spreadsheet_Chlamydia_20131125_KD.xls]]
:version edited during office hours by Dr. Dahlquist to demonstrate statistics
*[[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls]]
:finished version of version edited during office hours by Dr. Dahlquist to demonstrate statistics -- finished by Dillon Williams
*[[Media: Copy of Master Spreadsheet Chlamydia V2 20131203 HD.xls]]
:Microarray data with separated IDs CTA_#### from _RRMH#####_...
*[[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]]
:Excel Speadsheet with data formatted for GenMAPP (Version run in GenMAPP).

'''For GenMAPP Files'''
*[[Media: Ctrachomatis EbtoRb ATP metabolic process.mapp]]
: EB to RB ATP Metabolic Process Mapp file.
*[[Media: Ctrachomatis EbtoRB glucose catabolic process 20131204 DW.mapp]]
: EB to RB glucose catabolic process map.
*[[Media: CTrachomatis EBtoRB Rifampicin 20131204 DW-Criterion1-GO.txt]]
: EB to RB Rifampicin go.txt file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.gex]]
: For_GenMAPP .gex file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.gmf]]
: For GenMAPP .gmf file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.zip]]
: Access file created with .gex file.
*[[Media: For GenMAPP Chlamydia V4 20131205 KS.gex]]
:Color set created in GenMAPP for EB to RB no rifampicin and increased/decreased logFC criteria

'''MAPPFinder Files'''
*[[Media:EB to RB No Rif V2-Criterion0-GO.txt]]
:Increased
*[[Media: EB to RB No Rif V2-Criterion1-GO.txt]]
:Deceased
*[[Media: For GenMAPP Chlamydia V4 20131205 KS.gmf]]
: File created by MAPPFinder after creating the latest color set.

'''Final Excel Spreadsheet Containing Everything from GenMAPP and MAPPFinder'''
*Final Excel Sheet Used for Project.xls

==Wiki Formatting==

Template: [[Template:Team_H(oo)KD]]

[[Category: Group Projects]]
[[Category: Team H(oo)KD]]

File:Final Excel Sheet Used for Project.xls

2013-12-13T23:34:51Z

Dwilliams: Final excel sheet used for project. Includes all raw data, all EB to RB ratios in the presence and absence of rifampicin, statistical analysis of that data, for GenMAPP data, and all charts and tables used for GO terms and summaries of data.

Final excel sheet used for project. Includes all raw data, all EB to RB ratios in the presence and absence of rifampicin, statistical analysis of that data, for GenMAPP data, and all charts and tables used for GO terms and summaries of data.

Dwilliams Project Notebook

2013-12-12T00:27:30Z

Dwilliams: Formatting

==Week 12==
===Obtaining the Raw Data===
#Went to Arrayexpress website and downloaded all of the microarray raw data.
===Transferring Raw Data into Excel Sheet===
#Opened raw data in microsoft excel.
#Saved raw data in excel sheet format.
#Proceeded to upload all of the microarray raw data onto team wiki page.
#Determined sdrf sheet to contain gene ID's (discovered through a readme that was included on the arrayexrpess website.
#Opened the sdrf file in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.
===Reflection===
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Week 13==
===Preparing the Affymetrix and dChip Data===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
===Obtained dChip and Microarray Data===
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
===Basic steps to open expression data===
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
===Renaming Columns in Master Spreadsheet===
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
===Issues with Creating Master Excel Spreadsheet===
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].
==Week 14==
===Creating the EB to RB Sheet===
*Met with Dahlquist during office hours (11/26/2013).
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
===Creating EB to RB Rifampicin Sheet===
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.

==Week 15==
===Creating the For GenMAPP Sheet in Excel===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".
*Copied all CTA and pCTA ID's into column A.
*Titled column B "SystemCode".
**Typed "N" in row B2 and copied it down the entire column.
*Titled Column C "AverageEB" and copied the column (column H) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column C in "For_GenMAPP" sheet.
*Titled Column D "AverageRB" and copied the column (column I) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column D in "For_GenMAPP" sheet.
*Titled Column E "EB-to-RB" and copied the column (column J) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column E in "For_GenMAPP" sheet.
*Titled Column F "LogFC_EB-to-RB" and copied the column (column K) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column F in "For_GenMAPP" sheet.
*Titled Column G "P value" and copied the column (column L) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column G in "For_GenMAPP" sheet.
*Titled Column H "AverageEB Rifampicin" and copied the column (column I) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column H in "For_GenMAPP" sheet.
*Titled Column I "AverageRB Rifampicin" and copied the column (column J) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column I in "For_GenMAPP" sheet.
*Titled Column J "EB-to-RB Rifampicin" and copied the column (column K) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column J in "For_GenMAPP" sheet.
*Titled Column K "LogFC_EB-to-RB Rifampicin" and copied the column (column L) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column K in "For_GenMAPP" sheet.
*Titled Column L "P value Rifampicin" and copied the column (column M) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column L in "For_GenMAPP" sheet.
*Saved sheet as [[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]] found on team page.

{{dwilliams}}
[[Category:Journal Entry]]
[[Category:Individual Homework]]

User:Dwilliams

2013-12-07T22:11:02Z

Dwilliams: Formatting

== Contact Information ==

:1 LMU Drive MS B-8056
:Los Angeles, CA 90045
:dwilli67@lion.lmu.edu

== Education ==

'''Bachelor of Arts in Philosophy''' and '''Bachelor of Arts in Classics''' with '''Biochemistry Minor''', Loyola Marymount University, Expected Graduation in May 2015

*Upper Division Biochemistry Coursework
#Genetics
#Organic Chemistry and Lab

==Work Experience==

*'''Secretary for the Director of Pre-Medical Advising''', Loyola Marymount University, Los Angeles, CA, January 2012-May 2013.
**Scheduled appointments for the director over the phone.
**Organized pre-medical students as well as post-baccalaureate students files.
**Researched and read data for medical school acceptance rates and criteria by year and state and created excel spreadsheets to compile and organize data.
*'''Health Peer Educator''', Loyola Marymount University, Los Angeles, Ca, August 2012-Present
**Trained by and worked under the Director of Pre-Medical Advising.
**Advised undergraduate medical school applicants on the application process.

== Personal Interests ==

*Hiking
*Rock Climbing
*Swimming
*Music
*Creative Writing

{{dwilliams}}

== Template ==

[[Template:Dwilliams]]

[[Category: User Page]]

[[Category: Individual Homework]]

User:Dwilliams

2013-12-07T22:09:58Z

Dwilliams: Formatting

{{dwilliams}}

== Contact Information ==

:1 LMU Drive MS B-8056
:Los Angeles, CA 90045
:dwilli67@lion.lmu.edu

== Education ==

'''Bachelor of Arts in Philosophy''' and '''Bachelor of Arts in Classics''' with '''Biochemistry Minor''', Loyola Marymount University, Expected Graduation in May 2015

*Upper Division Biochemistry Coursework
#Genetics
#Organic Chemistry and Lab

==Work Experience==

*'''Secretary for the Director of Pre-Medical Advising''', Loyola Marymount University, Los Angeles, CA, January 2012-May 2013.
**Scheduled appointments for the director over the phone.
**Organized pre-medical students as well as post-baccalaureate students files.
**Researched and read data for medical school acceptance rates and criteria by year and state and created excel spreadsheets to compile and organize data.
*'''Health Peer Educator''', Loyola Marymount University, Los Angeles, Ca, August 2012-Present
**Trained by and worked under the Director of Pre-Medical Advising.
**Advised undergraduate medical school applicants on the application process.

== Personal Interests ==

*Hiking
*Rock Climbing
*Swimming
*Music
*Creative Writing

== Template ==

[[Template:Dwilliams]]

[[Category: User Page]]

[[Category: Individual Homework]]

User:Dwilliams

2013-12-07T22:06:03Z

Dwilliams: /* Education */ formatting

{{dwilliams}}
== Contact Information ==
:1 LMU Drive MS B-8056
:Los Angeles, CA 90045
:dwilli67@lion.lmu.edu

== Education ==

'''Bachelor of Arts in Philosophy''' and '''Bachelor of Arts in Classics''' with '''Biochemistry Minor''', Loyola Marymount University, Expected Graduation in May 2015

*Upper Division Biochemistry Coursework
#Genetics
#Organic Chemistry and Lab

==Work Experience==
*'''Secretary for the Director of Pre-Medical Advising''', Loyola Marymount University, Los Angeles, CA, January 2012-May 2013.
**Scheduled appointments for the director over the phone.
**Organized pre-medical students as well as post-baccalaureate students files.
**Researched and read data for medical school acceptance rates and criteria by year and state and created excel spreadsheets to compile and organize data.
*'''Health Peer Educator''', Loyola Marymount University, Los Angeles, Ca, August 2012-Present
**Trained by and worked under the Director of Pre-Medical Advising.
**Advised undergraduate medical school applicants on the application process.

== Personal Interests ==

*Hiking
*Rock Climbing
*Swimming
*Music
*Creative Writing

== Template ==

[[Template:Dwilliams]]

[[Category: User Page]]

[[Category: Individual Homework]]

User:Dwilliams

2013-12-07T22:00:39Z

Dwilliams: Formatting

{{dwilliams}}
== Contact Information ==
:1 LMU Drive MS B-8056
:Los Angeles, CA 90045
:dwilli67@lion.lmu.edu

== Education ==

'''Bachelor of Arts in Philosophy and Bachelor of Arts in Classics with Biochemistry Minor''', Loyola Marymount University, Expected Graduation in May 2015

*Upper Division Biochemistry Coursework
#Genetics
#Organic Chemistry and Lab

==Work Experience==
*'''Secretary for the Director of Pre-Medical Advising''', Loyola Marymount University, Los Angeles, CA, January 2012-May 2013.
**Scheduled appointments for the director over the phone.
**Organized pre-medical students as well as post-baccalaureate students files.
**Researched and read data for medical school acceptance rates and criteria by year and state and created excel spreadsheets to compile and organize data.
*'''Health Peer Educator''', Loyola Marymount University, Los Angeles, Ca, August 2012-Present
**Trained by and worked under the Director of Pre-Medical Advising.
**Advised undergraduate medical school applicants on the application process.

== Personal Interests ==

*Hiking
*Rock Climbing
*Swimming
*Music
*Creative Writing

== Template ==

[[Template:Dwilliams]]

[[Category: User Page]]

[[Category: Individual Homework]]

Dwilliams Project Notebook

2013-12-07T21:22:17Z

Dwilliams: /* Week 12 */ Formatting

{{dwilliams}}
==Week 12==
===Obtaining the Raw Data===
#Went to Arrayexpress website and downloaded all of the microarray raw data.
===Transferring Raw Data into Excel Sheet===
#Opened raw data in microsoft excel.
#Saved raw data in excel sheet format.
#Proceeded to upload all of the microarray raw data onto team wiki page.
#Determined sdrf sheet to contain gene ID's (discovered through a readme that was included on the arrayexrpess website.
#Opened the sdrf file in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.
===Reflection===
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Week 13==
===Preparing the Affymetrix and dChip Data===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
===Obtained dChip and Microarray Data===
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
===Basic steps to open expression data===
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
===Renaming Columns in Master Spreadsheet===
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
===Issues with Creating Master Excel Spreadsheet===
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].
==Week 14==
===Creating the EB to RB Sheet===
*Met with Dahlquist during office hours (11/26/2013).
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
===Creating EB to RB Rifampicin Sheet===
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.

==Week 15==
===Creating the For GenMAPP Sheet in Excel===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".
*Copied all CTA and pCTA ID's into column A.
*Titled column B "SystemCode".
**Typed "N" in row B2 and copied it down the entire column.
*Titled Column C "AverageEB" and copied the column (column H) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column C in "For_GenMAPP" sheet.
*Titled Column D "AverageRB" and copied the column (column I) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column D in "For_GenMAPP" sheet.
*Titled Column E "EB-to-RB" and copied the column (column J) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column E in "For_GenMAPP" sheet.
*Titled Column F "LogFC_EB-to-RB" and copied the column (column K) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column F in "For_GenMAPP" sheet.
*Titled Column G "P value" and copied the column (column L) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column G in "For_GenMAPP" sheet.
*Titled Column H "AverageEB Rifampicin" and copied the column (column I) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column H in "For_GenMAPP" sheet.
*Titled Column I "AverageRB Rifampicin" and copied the column (column J) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column I in "For_GenMAPP" sheet.
*Titled Column J "EB-to-RB Rifampicin" and copied the column (column K) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column J in "For_GenMAPP" sheet.
*Titled Column K "LogFC_EB-to-RB Rifampicin" and copied the column (column L) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column K in "For_GenMAPP" sheet.
*Titled Column L "P value Rifampicin" and copied the column (column M) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column L in "For_GenMAPP" sheet.
*Saved sheet as [[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]] found on team page.

[[Category:Journal Entry]]
[[Category:Individual Homework]]

Dwilliams Project Notebook

2013-12-07T21:16:06Z

Dwilliams: Formatting

{{dwilliams}}
==Week 12==
===Transferring Raw Data into Excel Sheet===
*Went to the Arrayexpress website and downloaded all of the microarray raw data.
*Proceeded to upload all of the microarray raw data onto team wiki page.
*I also opened the raw data in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.
===Reflection===
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Week 13==
===Preparing the Affymetrix and dChip Data===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
===Obtained dChip and Microarray Data===
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
===Basic steps to open expression data===
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
===Renaming Columns in Master Spreadsheet===
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
===Issues with Creating Master Excel Spreadsheet===
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].
==Week 14==
===Creating the EB to RB Sheet===
*Met with Dahlquist during office hours (11/26/2013).
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
===Creating EB to RB Rifampicin Sheet===
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.

==Week 15==
===Creating the For GenMAPP Sheet in Excel===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".
*Copied all CTA and pCTA ID's into column A.
*Titled column B "SystemCode".
**Typed "N" in row B2 and copied it down the entire column.
*Titled Column C "AverageEB" and copied the column (column H) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column C in "For_GenMAPP" sheet.
*Titled Column D "AverageRB" and copied the column (column I) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column D in "For_GenMAPP" sheet.
*Titled Column E "EB-to-RB" and copied the column (column J) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column E in "For_GenMAPP" sheet.
*Titled Column F "LogFC_EB-to-RB" and copied the column (column K) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column F in "For_GenMAPP" sheet.
*Titled Column G "P value" and copied the column (column L) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column G in "For_GenMAPP" sheet.
*Titled Column H "AverageEB Rifampicin" and copied the column (column I) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column H in "For_GenMAPP" sheet.
*Titled Column I "AverageRB Rifampicin" and copied the column (column J) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column I in "For_GenMAPP" sheet.
*Titled Column J "EB-to-RB Rifampicin" and copied the column (column K) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column J in "For_GenMAPP" sheet.
*Titled Column K "LogFC_EB-to-RB Rifampicin" and copied the column (column L) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column K in "For_GenMAPP" sheet.
*Titled Column L "P value Rifampicin" and copied the column (column M) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column L in "For_GenMAPP" sheet.
*Saved sheet as [[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]] found on team page.

[[Category:Journal Entry]]
[[Category:Individual Homework]]

Dwilliams Project Notebook

2013-12-07T21:12:32Z

Dwilliams: Formatting

{{dwilliams}}
==Electronic Lab Notebook Week 12==
===Transferring Raw Data into Excel Sheet===
*Went to the Arrayexpress website and downloaded all of the microarray raw data.
*Proceeded to upload all of the microarray raw data onto team wiki page.
*I also opened the raw data in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.
===Reflection===
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Electronic Lab Notebook Week 13==
===Preparing the Affymetrix and dChip Data===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
===Obtained dChip and Microarray Data===
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
===Basic steps to open expression data===
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
===Renaming Columns in Master Spreadsheet===
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
===Issues with Creating Master Excel Spreadsheet===
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].
==Electronic Lab Notebook Week 14==
===Creating the EB to RB Sheet===
*Met with Dahlquist during office hours (11/26/2013).
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
===Creating EB to RB Rifampicin Sheet===
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.

==Electronic Lab Notebook Week 15==
===Creating the For GenMAPP Sheet in Excel===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".
*Copied all CTA and pCTA ID's into column A.
*Titled column B "SystemCode".
**Typed "N" in row B2 and copied it down the entire column.
*Titled Column C "AverageEB" and copied the column (column H) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column C in "For_GenMAPP" sheet.
*Titled Column D "AverageRB" and copied the column (column I) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column D in "For_GenMAPP" sheet.
*Titled Column E "EB-to-RB" and copied the column (column J) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column E in "For_GenMAPP" sheet.
*Titled Column F "LogFC_EB-to-RB" and copied the column (column K) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column F in "For_GenMAPP" sheet.
*Titled Column G "P value" and copied the column (column L) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column G in "For_GenMAPP" sheet.
*Titled Column H "AverageEB Rifampicin" and copied the column (column I) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column H in "For_GenMAPP" sheet.
*Titled Column I "AverageRB Rifampicin" and copied the column (column J) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column I in "For_GenMAPP" sheet.
*Titled Column J "EB-to-RB Rifampicin" and copied the column (column K) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column J in "For_GenMAPP" sheet.
*Titled Column K "LogFC_EB-to-RB Rifampicin" and copied the column (column L) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column K in "For_GenMAPP" sheet.
*Titled Column L "P value Rifampicin" and copied the column (column M) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column L in "For_GenMAPP" sheet.
*Saved sheet as [[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]] found on team page.

[[Category:Journal Entry]]
[[Category:Individual Homework]]

Team H(oo)KD Week 15 Status Report

2013-12-06T08:41:51Z

Dwilliams: /* Reflection */ Formatting

{{Team H(oo)KD}}

'''Refer to the calendar on the team home page to see the milestones for this week.'''

==Coder Status Report==

The following was accomplished during Weeks 14-15:
*Determined why TallyEngine counted 917 genes in the gene database for ''C. trachomatis'' while the count was 919 when viewing the gene database in Access.
:*Apparently, one ordered locus ID (CTA_0406/CTA_0407/CTA_0408) is actually a combination of three ordered locus IDs each of which were predicted to correspond to a different gene before it was found that all three IDs actually correspond to the same gene. TallyEngine does not separate the ordered locus IDs while Access does.
:*In consulting with Dr. Dahlquist and Dr. Dionisio, we decided to leave this as is and describe the discrepancy in the final testing report, which is recorded in my [[Ksherbina Project Notebook|project journal]] under November 27-28, 2013.
*Customized the Tally Engine for ''C. trachomatis'' and committed the changes to SourceForge.

[[User:Ksherbina|Ksherbina]] ([[User talk:Ksherbina|talk]]) 22:41, 5 December 2013 (PST)

===Reflection===

#The Quality Assurance person (Hilda) and I were able to finish working on the gene database and figuring out how to separate the gene IDs from the Affymetrix IDs appened to the gene IDs in the microarray data. This allowed as to devote the rest of our time to working with Dillon to perform the GenMAPP and MAPPFinder analysis. Lucky for us, no exceptions file was generated when running GenMAPP with the microarray data with the modified IDs and the gene database for ''C. trachomatis''.
#When we originally set the milestones, we had planned to start working on both the paper and the presentation this week. Unfortunately, we had not advanced far enough in finalizing the database and performing GenMAPP analysis at the beginning of the week to be able to do this.
#With next week being finals week, we will have several meetings leading up to the final presentation in order to work on the paper, the presentation, and deliverables to make sure we meet the final deadline.

[[User:Ksherbina|Ksherbina]] ([[User talk:Ksherbina|talk]]) 23:02, 5 December 2013 (PST)

==Quality Assurance Status Report==
Katrina, the Coder, and I were able to work on separating the gene IDs so that statistical analysis could be performed by Dillon, the GenMAPP User, along with including this information into GenMAPP. The process of separating the IDs were tricky, but with Katrina's advice and some google searches I was able to manage separating the IDs, although I must admit it took Katrina 5 minutes to separate the IDs whereas it took me about close to an hour to figure out how to maneuver my way into figuring out how to go about this process. In any case, once this was done, Dillon (GenMAPP User) was able to generate the statistical analysis and the three of us proceeded to applying the data into GenMAPP. Luckily, we did not receive any errors throughout this transition to GenMAPP, so an exceptions file did not need to be generated. Moreover, we are now able to proceed with the project, so we will meet and start on our paper by Saturday. I will also proceed to complete the relational database schema for the gene database by Saturday. Katrina and I looked at the schema today and asked Dr. Dionisio questions about the schema to make sure we understood its format.

===Reflection===
#What worked?
#:Our schedules were able to match much better this week, so we were all able to meet without any problems.
#What didn't work?
#:We had hoped to start on the paper this week, but unfortunately we faced difficulties with the microarray data and gmbuilder, so we were not able to get far enough in the process to run GenMAPP earlier in the week.
#What will I do next to fix what didn't work?
#:We have resolved the problems we faced, so we will make sure to begin the paper as soon as possible (by Saturday) and if there are any questions we will contact Dr. Dionisio and Dr. Dahlquist immediately.

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 00:05, 6 December 2013 (PST)

==GenMAPP User Status Report==
This week, after fixing the initial issues that we had with running the statistics on the C. trachomatis raw data, I was able to create the final excel spreadsheet that was to be used in GenMAPP. With the help of the coder and QA in formatting the gene ID's for the "for GenMAPP" sheet in the excel master spreadhseet, I was able to create a sheet with all of the information necessary to run the data in GenMAPP.
*I used the database the Katrina (coder) created and proceeded to use the tab delimited file of the final excel spreadsheet to run the dataset in GenMAPP.
*We had no errors.
*After running GenMAPP, I used the LogFC changes and P values of the Rifampicin/No Rifampicin EB to RB data to create a color set. The color set was then saved as a .gex file on our team page.
*After completing this, Katrina and I used MAPPFinder to find the changes in some of the metabolic and catabolic pathways of the genes used.
*We are currently in the process of creating a map for the changes in these pathways.
===Reflection===
#) This week, I spent a lot of time sorting out a lot of little problems. When it came to some of the things that required collaboration of multiple group members, Katrina and I were able to get the work done fairly efficiently and we both spent a lot of time making sure that everything ran smoothly.
#) There wasn't anything that didn't work per se, although we did not get as much done as we were hoping for, we are going to continue working on the project over the course of the weekend.
#) Next week we will really be focusing our time and energy into ensuring that everything is done correctly and that the paper is done as well as possible. I personally, will also contribute time to cleaning up my electronic lab notebook, streamlining some of the steps and making the page itself more readable (I have already begun to improve some of the formatting on my page). Ultimately, next week will consist of tying off any loose ends and ensuring that everything is running how it should be running.
-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 22:07, 5 December 2013 (PST)

Team H(oo)KD Week 15 Status Report

2013-12-06T08:41:14Z

Dwilliams: /* Reflection */

Team H(oo)KD Week 15 Status Report

2013-12-06T08:40:55Z

Dwilliams: /* GenMAPP User Status Report */ Added GenMAPP

Chlamydia trachomatis

2013-12-05T19:38:52Z

Dwilliams: /* Important Files */ Added Files

{{Team_H(oo)KD}}

==Deadlines and Intermediate Milestones==

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 8em; background: #ddd" | Monday
! style="width: 8em; background: #ddd" | Tuesday
! style="width: 8em; background: #ddd" | Wednesday
! style="width: 8em; background: #ddd" | Thursday
! style="width: 8em; background: #ddd" | Friday
|-
| style="vertical-align: top" | 11/11
| style="vertical-align: top" | 11/12
| style="vertical-align: top" | 11/13
| style="vertical-align: top" | 11/14
*Run an export/import of gene database cycle '''KS/HD'''
*Create species profile '''KS'''
*Obtain and format raw microarray data '''DW'''
| style="vertical-align: top" | 11/15
*Rerun export/import of gene database cycle '''KS'''
|-
| style="vertical-align: top; background: #eee" | 11/18
| style="vertical-align: top; background: #eee" | 11/19
*Vet the gene database exported last week '''KS/HD/DW'''
*Format the raw microarray data '''DW'''
| style="vertical-align: top; background: #eee" | 11/20
| style="vertical-align: top; background: #eee" | 11/21
*Perform microarray statistical analysis '''DW'''
*Work on custom species profile '''KS/HD'''
| style="vertical-align: top; background: #eee" | 11/22
|-
| style="vertical-align: top" | 11/25
| style="vertical-align: top" | 11/26
*Build and commit species profile '''KS'''
*Customize Tally Engine '''KS/HD'''
*Perform GenMAPP and MAPPFinder Analysis '''DW'''
| style="vertical-align: top" | 11/27
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/28
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/29
'''THANKSGIVING BREAK'''
|-
| style="vertical-align: top; background: #eee" | 12/02
| style="vertical-align: top; background: #eee" | 12/03
*Run GenMAPP and MAPPFinder '''DW'''
*Customize the Tally Engine for ''C. trachomatis'' '''DW'''
| style="vertical-align: top; background: #eee" | 12/04
*Run GenMAPP and MAPPFinder again if necessary '''DW'''
| style="vertical-align: top; background: #eee" | 12/05
*Begin working on the relational database schema '''HD'''
*Commit the changes to gmbuilder '''KS'''
| style="vertical-align: top; background: #eee" | 12/06
|-
| style="vertical-align: top; background: #eee" | 12/09
*Write the paper '''HD/KS/DW'''
*Work on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/10
*Write the paper '''HD/KS/DW'''
*Work on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/11
*Finish the presentation '''HD/KS/DW'''
*Practice the final presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/12
*'''Final Presentation'''
*Proofread the final paper '''HD/KS/DW'''
*Make sure all the deliverables are raedy '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/13
|}

==Annotated Bibliography of Genomics Papers for ''C. trachomatis''==

===Whole genome sequencing of ''C. trachomatis''===

#Journal article describing results of whole genome sequencing:
#*Database: PubMed
#*Search Terms: Chlamydia trachomatis [MeSH Term] AND genome [Title]
#*There were 29 results. Many of the articles that appear using the above search terms have to do with performing whole-genome analysis of ''C. trachomatis'' to look at genetic polymorphisms in the bacterium and molecular and genetic characteristics that are observed when the bacterium infects a host.
#*Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R., Zhao, Q., Koonin, E. V., Davis, R.W. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. ''Science'' '''282''': 754-759. 10.1126/science.282.5389.754.
#*The article can be viewed as an [http://www.sciencemag.org/content/282/5389/754.long HTML].
#*The article can be viewed as a [[Media: Science-1998-Stephens-754-9.pdf | PDF]].
#*This article includes [http://www.sciencemag.org/site/feature/data/982604.xhtml Supplementary Material].
#Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
#*How many results did you get?: 872
#*Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?: Based on the titles and abstracts found in the results, it seems that research has been primarily in the direction of understanding how the disease functions and assessing the severity of the disease (and how to cure it).

===Microarray articles===
The EBI ArrayExpress database was used to locate each of the four following microarray articles. The search terms used were Chlamydia trachomatis under 'By organism' while the rest of the drop down menus were not altered.

The following articles appear in order of preference:

#Omsland, A., Sager, J., Nair, V., Sturdevant, D.E., Hackstadt, T. (2012) [http://www.pnas.org/content/109/48/19781.full Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]. ''PNAS'' '''109''': 19781-19785. doi: 10.1073/pnas.1212831109.
#*[[Media: PNAS-2012-Omsland-19781-5.pdf|PDF Version of Paper]]
#*[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data]
#*Chlamydiae undergo a biphasic developmental cycle characterized by an infectious cell type known as either an elementary body (EB) and an intracellular replicative form called a reticulate body (RB). Chlamydia was incubated under microaerobic conditions to test the differences in preferred energy source between EB's and RB's.
#*There weren't necessarily a "treatment" group and a "control" group. Referencing figure 4, it can be inferred that EB would be considered the "treatment" group because of the way that the ratio was set up, being EB to RB. In this way the RB would be the "control" group as they are looking at the EB population relative to the RB population.
#*4 Biological Replicates were performed for the control and treatment; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates...".


==Journal Club Presentation on ''C. trachomatis'' Genome Sequencing Paper==

[[Media:Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf|Here]] is the PDF version of the presentation given on November 12, 2013 on the Stephens ''et al.'' (1998) paper.


==Important Files==

*[[Media: Go_daily-termdb_v2_HD_20131107.obo-xml.gz|Go_daily-termdb_v2_HD_20131107.obo-xml.gz]]
:GO OBO-XML file for ''C. trachomatis'' serovar A.
*[[Media: Uniprot XML C.trachomatis serovar A KS 20131114.xml|Uniprot XML C.trachomatis serovar A KS 20131114.xml]]
:UniProt XML file for ''C. trachomatis'' serovar A.
*[[Media: 22183.C trachomatis A KS 20131114.goa|22183.C trachomatis A KS 20131114.goa]]
:GOA file for ''C. trachomatis'' serovar A.
*[[Media: Ct-Std v1 KS 20131119.gdb|Ct-Std v1 KS 20131119.gdb]]
:First iteration of the export/import gene database cycle.
*[[Media: Ct-Std KS 20131121.gdb|Ct-Std KS 20131121.gdb]]
:Updated gene database.
*[[Media: Ct-Std v2 KS 20131121.gdb|Ct-Std v2 KS 20131121.gdb]]
:New gene database created with the new version of gmbuilder built on 11/21/2013 using the custom species profile for ''C. trachomatis.''

'''Array Express Article Raw Files'''

*[[Media:Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt|Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt]]
:Microarray raw ADF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt]]
:Microarray raw IDF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip]]
:Microarray raw processed zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip]]
:Microarray raw zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt]]
:Microarray SDRF text file for ''C. trachomatis''.
*[[Media:Sdrf information excel.xls|Sdrf information excel.xls]]
:sdrf information in excel spreadsheet format.

'''Excel Master Spreadsheet File Versions (Containing the Formatted Raw Data)'''

*[[Media:Master Spreadsheet.xls|master spreadsheet work in progress]]
:Initial Microarray raw data formatted and opened in Microsoft Excel.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls]]
:Sample C. trachomatis microarray data that was used to run GenMAPP with the latest ''C. trachomatis'' database.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt]]
:Tab-delimited version of the file above.
*[[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]]
:Microarray data with identified Gene ID's and Log base data.
*[[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls | Master_Spreadsheet_Chlamydia_20131125_KD.xls]]
:version edited during office hours by Dr. Dahlquist to demonstrate statistics
*[[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls]]
:finished version of version edited during office hours by Dr. Dahlquist to demonstrate statistics -- finished by Dillon Williams
*[[Media: Copy of Master Spreadsheet Chlamydia V2 20131203 HD.xls]]
:Microarray data with separated IDs CTA_#### from _RRMH#####_...
*[[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]]
:Excel Speadsheet with data formatted for GenMAPP (Version run in GenMAPP).

'''For GenMAPP Files'''
*[[Media: Ctrachomatis EbtoRb ATP metabolic process.mapp]]
: EB to RB ATP Metabolic Process Mapp file.
*[[Media: Ctrachomatis EbtoRB glucose catabolic process 20131204 DW.mapp]]
: EB to RB glucose catabolic process map.
*[[Media: CTrachomatis EBtoRB Rifampicin 20131204 DW-Criterion1-GO.txt]]
: EB to RB Rifampicin go.txt file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.gex]]
: For_GenMAPP .gex file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.gmf]]
: For GenMAPP .gmf file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.zip]]
: Access file created with .gex file.
*[[Media: For GenMAPP Chlamydia V4 20131205 KS.gex]]
:Color set created in GenMAPP for EB to RB no rifampicin and increased/decreased logFC criteria

'''MAPPFinder Files'''
*[[Media:EB to RB No Rif V2-Criterion0-GO.txt]]
:Increased
*[[Media: EB to RB No Rif V2-Criterion1-GO.txt]]
:Deceased
*[[Media: For GenMAPP Chlamydia V4 20131205 KS.gmf]]
: File created by MAPPFinder after creating the latest color set.

==Wiki Formatting==

Template: [[Template:Team_H(oo)KD]]

[[Category: Group Projects]]
[[Category: Team H(oo)KD]]

File:For GenMAPP Chlamydia V4 20131205 KS.gmf

2013-12-05T19:37:23Z

Dwilliams: File created by MAPPFinder after creating the latest color set.

File created by MAPPFinder after creating the latest color set.

File:For GenMAPP Chlamydia V4 20131205 KS.gex

2013-12-05T19:36:46Z

Dwilliams: Color set created in GenMAPP for EB to RB no rifampicin and increased/decreased logFC criteria

Color set created in GenMAPP for EB to RB no rifampicin and increased/decreased logFC criteria

Chlamydia trachomatis

2013-12-05T19:33:02Z

Dwilliams: /* Important Files */ Added Files

{{Team_H(oo)KD}}

==Deadlines and Intermediate Milestones==

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 8em; background: #ddd" | Monday
! style="width: 8em; background: #ddd" | Tuesday
! style="width: 8em; background: #ddd" | Wednesday
! style="width: 8em; background: #ddd" | Thursday
! style="width: 8em; background: #ddd" | Friday
|-
| style="vertical-align: top" | 11/11
| style="vertical-align: top" | 11/12
| style="vertical-align: top" | 11/13
| style="vertical-align: top" | 11/14
*Run an export/import of gene database cycle '''KS/HD'''
*Create species profile '''KS'''
*Obtain and format raw microarray data '''DW'''
| style="vertical-align: top" | 11/15
*Rerun export/import of gene database cycle '''KS'''
|-
| style="vertical-align: top; background: #eee" | 11/18
| style="vertical-align: top; background: #eee" | 11/19
*Vet the gene database exported last week '''KS/HD/DW'''
*Format the raw microarray data '''DW'''
| style="vertical-align: top; background: #eee" | 11/20
| style="vertical-align: top; background: #eee" | 11/21
*Perform microarray statistical analysis '''DW'''
*Work on custom species profile '''KS/HD'''
| style="vertical-align: top; background: #eee" | 11/22
|-
| style="vertical-align: top" | 11/25
| style="vertical-align: top" | 11/26
*Build and commit species profile '''KS'''
*Customize Tally Engine '''KS/HD'''
*Perform GenMAPP and MAPPFinder Analysis '''DW'''
| style="vertical-align: top" | 11/27
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/28
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/29
'''THANKSGIVING BREAK'''
|-
| style="vertical-align: top; background: #eee" | 12/02
| style="vertical-align: top; background: #eee" | 12/03
*Run GenMAPP and MAPPFinder '''DW'''
*Customize the Tally Engine for ''C. trachomatis'' '''DW'''
| style="vertical-align: top; background: #eee" | 12/04
*Run GenMAPP and MAPPFinder again if necessary '''DW'''
| style="vertical-align: top; background: #eee" | 12/05
*Begin working on the relational database schema '''HD'''
*Commit the changes to gmbuilder '''KS'''
| style="vertical-align: top; background: #eee" | 12/06
|-
| style="vertical-align: top; background: #eee" | 12/09
*Write the paper '''HD/KS/DW'''
*Work on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/10
*Write the paper '''HD/KS/DW'''
*Work on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/11
*Finish the presentation '''HD/KS/DW'''
*Practice the final presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/12
*'''Final Presentation'''
*Proofread the final paper '''HD/KS/DW'''
*Make sure all the deliverables are raedy '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/13
|}

==Annotated Bibliography of Genomics Papers for ''C. trachomatis''==

===Whole genome sequencing of ''C. trachomatis''===

#Journal article describing results of whole genome sequencing:
#*Database: PubMed
#*Search Terms: Chlamydia trachomatis [MeSH Term] AND genome [Title]
#*There were 29 results. Many of the articles that appear using the above search terms have to do with performing whole-genome analysis of ''C. trachomatis'' to look at genetic polymorphisms in the bacterium and molecular and genetic characteristics that are observed when the bacterium infects a host.
#*Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R., Zhao, Q., Koonin, E. V., Davis, R.W. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. ''Science'' '''282''': 754-759. 10.1126/science.282.5389.754.
#*The article can be viewed as an [http://www.sciencemag.org/content/282/5389/754.long HTML].
#*The article can be viewed as a [[Media: Science-1998-Stephens-754-9.pdf | PDF]].
#*This article includes [http://www.sciencemag.org/site/feature/data/982604.xhtml Supplementary Material].
#Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
#*How many results did you get?: 872
#*Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?: Based on the titles and abstracts found in the results, it seems that research has been primarily in the direction of understanding how the disease functions and assessing the severity of the disease (and how to cure it).

===Microarray articles===
The EBI ArrayExpress database was used to locate each of the four following microarray articles. The search terms used were Chlamydia trachomatis under 'By organism' while the rest of the drop down menus were not altered.

The following articles appear in order of preference:

#Omsland, A., Sager, J., Nair, V., Sturdevant, D.E., Hackstadt, T. (2012) [http://www.pnas.org/content/109/48/19781.full Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]. ''PNAS'' '''109''': 19781-19785. doi: 10.1073/pnas.1212831109.
#*[[Media: PNAS-2012-Omsland-19781-5.pdf|PDF Version of Paper]]
#*[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data]
#*Chlamydiae undergo a biphasic developmental cycle characterized by an infectious cell type known as either an elementary body (EB) and an intracellular replicative form called a reticulate body (RB). Chlamydia was incubated under microaerobic conditions to test the differences in preferred energy source between EB's and RB's.
#*There weren't necessarily a "treatment" group and a "control" group. Referencing figure 4, it can be inferred that EB would be considered the "treatment" group because of the way that the ratio was set up, being EB to RB. In this way the RB would be the "control" group as they are looking at the EB population relative to the RB population.
#*4 Biological Replicates were performed for the control and treatment; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates...".


==Journal Club Presentation on ''C. trachomatis'' Genome Sequencing Paper==

[[Media:Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf|Here]] is the PDF version of the presentation given on November 12, 2013 on the Stephens ''et al.'' (1998) paper.


==Important Files==

*[[Media: Go_daily-termdb_v2_HD_20131107.obo-xml.gz|Go_daily-termdb_v2_HD_20131107.obo-xml.gz]]
:GO OBO-XML file for ''C. trachomatis'' serovar A.
*[[Media: Uniprot XML C.trachomatis serovar A KS 20131114.xml|Uniprot XML C.trachomatis serovar A KS 20131114.xml]]
:UniProt XML file for ''C. trachomatis'' serovar A.
*[[Media: 22183.C trachomatis A KS 20131114.goa|22183.C trachomatis A KS 20131114.goa]]
:GOA file for ''C. trachomatis'' serovar A.
*[[Media: Ct-Std v1 KS 20131119.gdb|Ct-Std v1 KS 20131119.gdb]]
:First iteration of the export/import gene database cycle.
*[[Media: Ct-Std KS 20131121.gdb|Ct-Std KS 20131121.gdb]]
:Updated gene database.
*[[Media: Ct-Std v2 KS 20131121.gdb|Ct-Std v2 KS 20131121.gdb]]
:New gene database created with the new version of gmbuilder built on 11/21/2013 using the custom species profile for ''C. trachomatis.''

'''Array Express Article Raw Files'''

*[[Media:Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt|Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt]]
:Microarray raw ADF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt]]
:Microarray raw IDF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip]]
:Microarray raw processed zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip]]
:Microarray raw zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt]]
:Microarray SDRF text file for ''C. trachomatis''.
*[[Media:Sdrf information excel.xls|Sdrf information excel.xls]]
:sdrf information in excel spreadsheet format.

'''Excel Master Spreadsheet File Versions (Containing the Formatted Raw Data)'''

*[[Media:Master Spreadsheet.xls|master spreadsheet work in progress]]
:Initial Microarray raw data formatted and opened in Microsoft Excel.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls]]
:Sample C. trachomatis microarray data that was used to run GenMAPP with the latest ''C. trachomatis'' database.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt]]
:Tab-delimited version of the file above.
*[[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]]
:Microarray data with identified Gene ID's and Log base data.
*[[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls | Master_Spreadsheet_Chlamydia_20131125_KD.xls]]
:version edited during office hours by Dr. Dahlquist to demonstrate statistics
*[[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls]]
:finished version of version edited during office hours by Dr. Dahlquist to demonstrate statistics -- finished by Dillon Williams
*[[Media: Copy of Master Spreadsheet Chlamydia V2 20131203 HD.xls]]
:Microarray data with separated IDs CTA_#### from _RRMH#####_...
*[[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]]
:Excel Speadsheet with data formatted for GenMAPP (Version run in GenMAPP).

'''For GenMAPP Files'''
*[[Media: Ctrachomatis EbtoRb ATP metabolic process.mapp]]
: EB to RB ATP Metabolic Process Mapp file.
*[[Media: Ctrachomatis EbtoRB glucose catabolic process 20131204 DW.mapp]]
: EB to RB glucose catabolic process map.
*[[Media: CTrachomatis EBtoRB Rifampicin 20131204 DW-Criterion1-GO.txt]]
: EB to RB Rifampicin go.txt file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.gex]]
: For_GenMAPP .gex file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.gmf]]
: For GenMAPP .gmf file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.zip]]
: Access file created with .gex file.

'''MAPPFinder Files'''
*[[Media:EB to RB No Rif V2-Criterion0-GO.txt]]
:Increased
*[[Media: EB to RB No Rif V2-Criterion1-GO.txt]]
:Deceased

==Wiki Formatting==

Template: [[Template:Team_H(oo)KD]]

[[Category: Group Projects]]
[[Category: Team H(oo)KD]]

File:EB to RB No Rif V2-Criterion1-GO.txt

2013-12-05T19:31:19Z

Dwilliams: Deceased

Deceased

File:EB to RB No Rif V2-Criterion0-GO.txt

2013-12-05T19:31:04Z

Dwilliams: Increased

Increased

Dwilliams Project Notebook

2013-12-05T19:13:45Z

Dwilliams: /* Meeting with Dahlquist (11/26/2013) */ Formatting

==Electronic Lab Notebook Week 12==
===Transferring Raw Data into Excel Sheet===
*Went to the Arrayexpress website and downloaded all of the microarray raw data.
*Proceeded to upload all of the microarray raw data onto team wiki page.
*I also opened the raw data in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.
===Reflection===
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Electronic Lab Notebook Week 13==
===Preparing the Affymetrix and dChip Data===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
===Obtained dChip and Microarray Data===
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
===Basic steps to open expression data===
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
===Renaming Columns in Master Spreadsheet===
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
===Issues with Creating Master Excel Spreadsheet===
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].
==Electronic Lab Notebook Week 14==
===Creating the EB to RB Sheet===
*Met with Dahlquist during office hours (11/26/2013).
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
===Creating EB to RB Rifampicin Sheet===
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.

==Electronic Lab Notebook Week 15==
===Creating the For GenMAPP Sheet in Excel===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".
*Copied all CTA and pCTA ID's into column A.
*Titled column B "SystemCode".
**Typed "N" in row B2 and copied it down the entire column.
*Titled Column C "AverageEB" and copied the column (column H) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column C in "For_GenMAPP" sheet.
*Titled Column D "AverageRB" and copied the column (column I) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column D in "For_GenMAPP" sheet.
*Titled Column E "EB-to-RB" and copied the column (column J) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column E in "For_GenMAPP" sheet.
*Titled Column F "LogFC_EB-to-RB" and copied the column (column K) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column F in "For_GenMAPP" sheet.
*Titled Column G "P value" and copied the column (column L) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column G in "For_GenMAPP" sheet.
*Titled Column H "AverageEB Rifampicin" and copied the column (column I) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column H in "For_GenMAPP" sheet.
*Titled Column I "AverageRB Rifampicin" and copied the column (column J) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column I in "For_GenMAPP" sheet.
*Titled Column J "EB-to-RB Rifampicin" and copied the column (column K) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column J in "For_GenMAPP" sheet.
*Titled Column K "LogFC_EB-to-RB Rifampicin" and copied the column (column L) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column K in "For_GenMAPP" sheet.
*Titled Column L "P value Rifampicin" and copied the column (column M) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column L in "For_GenMAPP" sheet.
*Saved sheet as [[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]] found on team page.

[[Category:Journal Entry]]
[[Category:Individual Homework]]

Dwilliams Project Notebook

2013-12-05T19:10:31Z

Dwilliams: Formatting

==Electronic Lab Notebook Week 12==
===Transferring Raw Data into Excel Sheet===
*Went to the Arrayexpress website and downloaded all of the microarray raw data.
*Proceeded to upload all of the microarray raw data onto team wiki page.
*I also opened the raw data in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.
===Reflection===
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Electronic Lab Notebook Week 13==
===Preparing the Affymetrix and dChip Data===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
===Obtained dChip and Microarray Data===
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
===Basic steps to open expression data===
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
===Renaming Columns in Master Spreadsheet===
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
===Issues with Creating Master Excel Spreadsheet===
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].
==Electronic Lab Notebook Week 14==
===Meeting with Dahlquist (11/26/2013)===
*Met with Dahlquist during office hours.
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.
==Electronic Lab Notebook Week 15==
===Creating the For GenMAPP Sheet in Excel===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".
*Copied all CTA and pCTA ID's into column A.
*Titled column B "SystemCode".
**Typed "N" in row B2 and copied it down the entire column.
*Titled Column C "AverageEB" and copied the column (column H) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column C in "For_GenMAPP" sheet.
*Titled Column D "AverageRB" and copied the column (column I) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column D in "For_GenMAPP" sheet.
*Titled Column E "EB-to-RB" and copied the column (column J) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column E in "For_GenMAPP" sheet.
*Titled Column F "LogFC_EB-to-RB" and copied the column (column K) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column F in "For_GenMAPP" sheet.
*Titled Column G "P value" and copied the column (column L) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column G in "For_GenMAPP" sheet.
*Titled Column H "AverageEB Rifampicin" and copied the column (column I) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column H in "For_GenMAPP" sheet.
*Titled Column I "AverageRB Rifampicin" and copied the column (column J) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column I in "For_GenMAPP" sheet.
*Titled Column J "EB-to-RB Rifampicin" and copied the column (column K) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column J in "For_GenMAPP" sheet.
*Titled Column K "LogFC_EB-to-RB Rifampicin" and copied the column (column L) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column K in "For_GenMAPP" sheet.
*Titled Column L "P value Rifampicin" and copied the column (column M) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column L in "For_GenMAPP" sheet.
*Saved sheet as [[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]] found on team page.

[[Category:Journal Entry]]
[[Category:Individual Homework]]

Dwilliams Project Notebook

2013-12-05T19:08:35Z

Dwilliams: Formatting

==Electronic Lab Notebook Week 12==
===Transferring Raw Data into Excel Sheet===
*Went to the Arrayexpress website and downloaded all of the microarray raw data.
*Proceeded to upload all of the microarray raw data onto team wiki page.
*I also opened the raw data in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.
===Reflection===
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Electronic Lab Notebook Week 13==
===Preparing the Affymetrix and dChip Data===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
===Obtained dChip and Microarray Data===
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
===Basic steps to open expression data===
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
===Renaming Columns in Master Spreadsheet===
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
===Issues with Creating Master Excel Spreadsheet===
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].
==Week 14==
===Electronic Lab Notebook Week 14 (11/26/2013)===
*Met with Dahlquist during office hours.
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.
==Week 15==
===Electronic Lab Notebook Week 15===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".
*Copied all CTA and pCTA ID's into column A.
*Titled column B "SystemCode".
**Typed "N" in row B2 and copied it down the entire column.
*Titled Column C "AverageEB" and copied the column (column H) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column C in "For_GenMAPP" sheet.
*Titled Column D "AverageRB" and copied the column (column I) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column D in "For_GenMAPP" sheet.
*Titled Column E "EB-to-RB" and copied the column (column J) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column E in "For_GenMAPP" sheet.
*Titled Column F "LogFC_EB-to-RB" and copied the column (column K) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column F in "For_GenMAPP" sheet.
*Titled Column G "P value" and copied the column (column L) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column G in "For_GenMAPP" sheet.
*Titled Column H "AverageEB Rifampicin" and copied the column (column I) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column H in "For_GenMAPP" sheet.
*Titled Column I "AverageRB Rifampicin" and copied the column (column J) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column I in "For_GenMAPP" sheet.
*Titled Column J "EB-to-RB Rifampicin" and copied the column (column K) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column J in "For_GenMAPP" sheet.
*Titled Column K "LogFC_EB-to-RB Rifampicin" and copied the column (column L) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column K in "For_GenMAPP" sheet.
*Titled Column L "P value Rifampicin" and copied the column (column M) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column L in "For_GenMAPP" sheet.
*Saved sheet as [[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]] found on team page.

[[Category:Journal Entry]]
[[Category:Individual Homework]]

Dwilliams Project Notebook

2013-12-05T19:05:49Z

Dwilliams: Formatting

==Electronic Lab Notebook Week 12==
===Transferring Raw Data into Excel Sheet===
*Went to the Arrayexpress website and downloaded all of the microarray raw data.
*Proceeded to upload all of the microarray raw data onto team wiki page.
*I also opened the raw data in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.
===Reflection===
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Week 13==
===Electronic Lab Notebook Week 13===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
**'''Obtained dChip and Microarray Data'''
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
**'''Basic steps to open expression data'''
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
**'''Renaming Columns in Master Spreadsheet'''
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
**'''Issues with Creating Master Excel Spreadsheet'''
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].
==Week 14==
===Electronic Lab Notebook Week 14 (11/26/2013)===
*Met with Dahlquist during office hours.
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.
==Week 15==
===Electronic Lab Notebook Week 15===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".
*Copied all CTA and pCTA ID's into column A.
*Titled column B "SystemCode".
**Typed "N" in row B2 and copied it down the entire column.
*Titled Column C "AverageEB" and copied the column (column H) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column C in "For_GenMAPP" sheet.
*Titled Column D "AverageRB" and copied the column (column I) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column D in "For_GenMAPP" sheet.
*Titled Column E "EB-to-RB" and copied the column (column J) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column E in "For_GenMAPP" sheet.
*Titled Column F "LogFC_EB-to-RB" and copied the column (column K) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column F in "For_GenMAPP" sheet.
*Titled Column G "P value" and copied the column (column L) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column G in "For_GenMAPP" sheet.
*Titled Column H "AverageEB Rifampicin" and copied the column (column I) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column H in "For_GenMAPP" sheet.
*Titled Column I "AverageRB Rifampicin" and copied the column (column J) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column I in "For_GenMAPP" sheet.
*Titled Column J "EB-to-RB Rifampicin" and copied the column (column K) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column J in "For_GenMAPP" sheet.
*Titled Column K "LogFC_EB-to-RB Rifampicin" and copied the column (column L) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column K in "For_GenMAPP" sheet.
*Titled Column L "P value Rifampicin" and copied the column (column M) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column L in "For_GenMAPP" sheet.
*Saved sheet as [[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]] found on team page.

[[Category:Journal Entry]]
[[Category:Individual Homework]]

Template:Dwilliams

2013-12-05T19:03:27Z

Dwilliams: Added Week Assignment Description

<div style="background: #00308F; padding: 10px; font-weight:bold; font-size:200%;color:white"><center>Dillon Williams</center></div>

<div style="background: #F0F8FF; padding: 10px">
<div style="font-weight:bold; font-size:130%"><center>[[Main Page|<span style="color:black;">'''Class Page'''</span>]]    [[User:dwilliams|<span style="color:black;">'''User Page'''</span>]] </center></div>

<div style="border-width: 2px; border-bottom-width:2px; border-bottom-color:#BEBEBE; border-bottom-style: solid; width: 100%"></div>

{| style = "width:60%; font-size:100%"
| '''Assignment Description'''
| '''[[Week 1]]'''
| '''[[Week 2]]'''
| '''[[Week 3]]'''
| '''[[Week 4]]'''
| '''[[Week 5]]'''
| '''[[Week 6]]'''
| '''[[Week 7]]'''
| '''[[Week 8]]'''
| '''[[Week 9]]'''
| '''[[Week 10]]'''
| '''[[Week 11]]'''
| '''[[Week 12]]'''
| '''[[Week 13]]'''
| '''[[Week 15]]'''
|-
| '''Class Journal'''
| '''[[Class Journal Week 1|Week 1]]'''
| '''[[Class Journal Week 2|Week 2]]'''
| '''[[Class Journal Week 3|Week 3]]'''
| '''[[Class Journal Week 4|Week 4]]'''
| '''[[Class Journal Week 5|Week 5]]'''
| '''[[Class Journal Week 6|Week 6]]'''
| '''[[Class Journal Week 7|Week 7]]'''
| '''[[Class Journal Week 8|Week 8]]'''
| '''[[Class Journal Week 9|Week 9]]'''
|-
| '''Individual Journal'''
| '''[[dwilliams Week 2|Week 2]]'''
| '''[[dwilliams week 3|Week 3]]'''
| '''[[dwilliams week 4 assignment|Week 4]]'''
| '''[[dwilliams week 5 assignment|Week 5]]'''
| '''[[dwilliams week 6 assignment|Week 6]]'''
| '''[[dwilliams week 7 assignment|Week 7]]'''
| '''[[dwilliams Week 8 assignment|Week 8]]'''
| '''[[dwilliams Week 9 assignment|Week 9]]'''
| '''[[dwilliams Week 10 assignment|Week 10]]'''
| '''[[dwilliams Week 11 assignment|Week 11]]'''
|-
| '''In Class Notes'''
| '''[[In Class Notes Week 11|Week 11]]'''
|}

{| style = "width:115%; font-size:100%"
| '''Final Project'''
| '''[[Chlamydia trachomatis|Team H(oo)KD Project Page]]'''
| '''[[Media:Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf|Journal Club Presentation]]
| '''[[dwilliams Project Notebook|Project Individual Journal]]'''
|}

[[Category:Journal Entry]]

[[Category:Shared]]

Dwilliams Project Notebook

2013-12-05T18:58:17Z

Dwilliams: Formatting

==Week 12==
===Electronic Lab Notebook Week 12===
*'''Transferring Raw Data into Excel Sheet'''
**Went to the Arrayexpress website and downloaded all of the microarray raw data.
**Proceeded to upload all of the microarray raw data onto team wiki page.
**I also opened the raw data in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.

*'''Reflection'''
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Week 13==
===Electronic Lab Notebook Week 13===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
**'''Obtained dChip and Microarray Data'''
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
**'''Basic steps to open expression data'''
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
**'''Renaming Columns in Master Spreadsheet'''
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
**'''Issues with Creating Master Excel Spreadsheet'''
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].
==Week 14==
===Electronic Lab Notebook Week 14 (11/26/2013)===
*Met with Dahlquist during office hours.
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.
==Week 15==
===Electronic Lab Notebook Week 15===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".
*Copied all CTA and pCTA ID's into column A.
*Titled column B "SystemCode".
**Typed "N" in row B2 and copied it down the entire column.
*Titled Column C "AverageEB" and copied the column (column H) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column C in "For_GenMAPP" sheet.
*Titled Column D "AverageRB" and copied the column (column I) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column D in "For_GenMAPP" sheet.
*Titled Column E "EB-to-RB" and copied the column (column J) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column E in "For_GenMAPP" sheet.
*Titled Column F "LogFC_EB-to-RB" and copied the column (column K) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column F in "For_GenMAPP" sheet.
*Titled Column G "P value" and copied the column (column L) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column G in "For_GenMAPP" sheet.
*Titled Column H "AverageEB Rifampicin" and copied the column (column I) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column H in "For_GenMAPP" sheet.
*Titled Column I "AverageRB Rifampicin" and copied the column (column J) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column I in "For_GenMAPP" sheet.
*Titled Column J "EB-to-RB Rifampicin" and copied the column (column K) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column J in "For_GenMAPP" sheet.
*Titled Column K "LogFC_EB-to-RB Rifampicin" and copied the column (column L) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column K in "For_GenMAPP" sheet.
*Titled Column L "P value Rifampicin" and copied the column (column M) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column L in "For_GenMAPP" sheet.
*Saved sheet as [[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]] found on team page.

[[Category:Journal Entry]]
[[Category:Individual Homework]]

Dwilliams Project Notebook

2013-12-05T18:43:15Z

Dwilliams: /* Electronic Lab Notebook Week 15 */ Fixed Link

==Week 12==
===Electronic Lab Notebook Week 12===
*'''Transferring Raw Data into Excel Sheet'''
**Went to the Arrayexpress website and downloaded all of the microarray raw data.
**Proceeded to upload all of the microarray raw data onto team wiki page.
**I also opened the raw data in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.

*'''Reflection'''
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Week 13==
===Electronic Lab Notebook Week 13===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
**'''Obtained dChip and Microarray Data'''
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
**'''Basic steps to open expression data'''
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
**'''Renaming Columns in Master Spreadsheet'''
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
**'''Issues with Creating Master Excel Spreadsheet'''
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].

===Electronic Lab Notebook Week 14 (11/26/2013)===
*Met with Dahlquist during office hours.
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.

===Electronic Lab Notebook Week 15===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".
*Copied all CTA and pCTA ID's into column A.
*Titled column B "SystemCode".
**Typed "N" in row B2 and copied it down the entire column.
*Titled Column C "AverageEB" and copied the column (column H) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column C in "For_GenMAPP" sheet.
*Titled Column D "AverageRB" and copied the column (column I) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column D in "For_GenMAPP" sheet.
*Titled Column E "EB-to-RB" and copied the column (column J) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column E in "For_GenMAPP" sheet.
*Titled Column F "LogFC_EB-to-RB" and copied the column (column K) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column F in "For_GenMAPP" sheet.
*Titled Column G "P value" and copied the column (column L) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column G in "For_GenMAPP" sheet.
*Titled Column H "AverageEB Rifampicin" and copied the column (column I) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column H in "For_GenMAPP" sheet.
*Titled Column I "AverageRB Rifampicin" and copied the column (column J) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column I in "For_GenMAPP" sheet.
*Titled Column J "EB-to-RB Rifampicin" and copied the column (column K) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column J in "For_GenMAPP" sheet.
*Titled Column K "LogFC_EB-to-RB Rifampicin" and copied the column (column L) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column K in "For_GenMAPP" sheet.
*Titled Column L "P value Rifampicin" and copied the column (column M) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column L in "For_GenMAPP" sheet.
*Saved sheet as [[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]] found on team page.

[[Category:Journal Entry]]
[[Category:Individual Homework]]

Dwilliams Project Notebook

2013-12-05T18:42:43Z

Dwilliams: /* Electronic Lab Notebook Week 15 */ Added steps and link

==Week 12==
===Electronic Lab Notebook Week 12===
*'''Transferring Raw Data into Excel Sheet'''
**Went to the Arrayexpress website and downloaded all of the microarray raw data.
**Proceeded to upload all of the microarray raw data onto team wiki page.
**I also opened the raw data in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.

*'''Reflection'''
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Week 13==
===Electronic Lab Notebook Week 13===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
**'''Obtained dChip and Microarray Data'''
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
**'''Basic steps to open expression data'''
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
**'''Renaming Columns in Master Spreadsheet'''
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
**'''Issues with Creating Master Excel Spreadsheet'''
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].

===Electronic Lab Notebook Week 14 (11/26/2013)===
*Met with Dahlquist during office hours.
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.

===Electronic Lab Notebook Week 15===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".
*Copied all CTA and pCTA ID's into column A.
*Titled column B "SystemCode".
**Typed "N" in row B2 and copied it down the entire column.
*Titled Column C "AverageEB" and copied the column (column H) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column C in "For_GenMAPP" sheet.
*Titled Column D "AverageRB" and copied the column (column I) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column D in "For_GenMAPP" sheet.
*Titled Column E "EB-to-RB" and copied the column (column J) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column E in "For_GenMAPP" sheet.
*Titled Column F "LogFC_EB-to-RB" and copied the column (column K) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column F in "For_GenMAPP" sheet.
*Titled Column G "P value" and copied the column (column L) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column G in "For_GenMAPP" sheet.
*Titled Column H "AverageEB Rifampicin" and copied the column (column I) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column H in "For_GenMAPP" sheet.
*Titled Column I "AverageRB Rifampicin" and copied the column (column J) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column I in "For_GenMAPP" sheet.
*Titled Column J "EB-to-RB Rifampicin" and copied the column (column K) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column J in "For_GenMAPP" sheet.
*Titled Column K "LogFC_EB-to-RB Rifampicin" and copied the column (column L) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column K in "For_GenMAPP" sheet.
*Titled Column L "P value Rifampicin" and copied the column (column M) from sheet "EB-to-RB_rif".
**Selected paste-->Paste Special-->Values into column L in "For_GenMAPP" sheet.
*Saved sheet as [[Media: Media: For GenMAPP Chlamydia V4 20131203 DW.xls]] found on team page
[[Category:Journal Entry]]
[[Category:Individual Homework]]

Dwilliams Project Notebook

2013-12-05T18:27:38Z

Dwilliams: /* Electronic Lab Notebook Week 15 */ Added Steps

==Week 12==
===Electronic Lab Notebook Week 12===
*'''Transferring Raw Data into Excel Sheet'''
**Went to the Arrayexpress website and downloaded all of the microarray raw data.
**Proceeded to upload all of the microarray raw data onto team wiki page.
**I also opened the raw data in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.

*'''Reflection'''
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Week 13==
===Electronic Lab Notebook Week 13===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
**'''Obtained dChip and Microarray Data'''
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
**'''Basic steps to open expression data'''
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
**'''Renaming Columns in Master Spreadsheet'''
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
**'''Issues with Creating Master Excel Spreadsheet'''
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].

===Electronic Lab Notebook Week 14 (11/26/2013)===
*Met with Dahlquist during office hours.
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.

===Electronic Lab Notebook Week 15===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".
*Copied all CTA and pCTA ID's into column A.
*Titled column B "SystemCode".
**Typed "N" in row B2 and copied it down the entire column.
*Titled Column C "AverageEB" and copied the column (column H) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column C in "For_GenMAPP" sheet.
Titled Column D "AverageRB" and copied the column (column I) from sheet "EB-to-RB".
**Selected paste-->Paste Special-->Values into column D in "For_GenMAPP" sheet.

[[Category:Journal Entry]]
[[Category:Individual Homework]]

Dwilliams Project Notebook

2013-12-05T18:22:31Z

Dwilliams: /* Electronic Lab Notebook Week 13 (11/26/2013) */ Fixed Date

==Week 12==
===Electronic Lab Notebook Week 12===
*'''Transferring Raw Data into Excel Sheet'''
**Went to the Arrayexpress website and downloaded all of the microarray raw data.
**Proceeded to upload all of the microarray raw data onto team wiki page.
**I also opened the raw data in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.

*'''Reflection'''
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Week 13==
===Electronic Lab Notebook Week 13===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
**'''Obtained dChip and Microarray Data'''
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
**'''Basic steps to open expression data'''
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
**'''Renaming Columns in Master Spreadsheet'''
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
**'''Issues with Creating Master Excel Spreadsheet'''
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].

===Electronic Lab Notebook Week 14 (11/26/2013)===
*Met with Dahlquist during office hours.
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.

===Electronic Lab Notebook Week 15===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".

[[Category:Journal Entry]]
[[Category:Individual Homework]]

Dwilliams Project Notebook

2013-12-05T18:21:32Z

Dwilliams: /* Electronic Lab Notebook Week 13 11/26/2013 */ Added Date

==Week 12==
===Electronic Lab Notebook Week 12===
*'''Transferring Raw Data into Excel Sheet'''
**Went to the Arrayexpress website and downloaded all of the microarray raw data.
**Proceeded to upload all of the microarray raw data onto team wiki page.
**I also opened the raw data in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.

*'''Reflection'''
#What were the week’s key accomplishments?
#*We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
#What are next week’s target accomplishments?
#*Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
#What team strengths were seen this week?
#*We worked well as a group and held a good level of communication with each other throughout the process.
#What team weaknesses were seen this week?
#*We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

==Week 13==
===Electronic Lab Notebook Week 13===
*Downloaded Affymetrix software from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
*Clicked on tutorial hyperlink from [https://sites.google.com/site/dchipsoft/home dChip web site].
*Opened "dChip expression data analysis" word doc.
*Begin following steps from word doc.:
**'''Obtained dChip and Microarray Data'''
*#Downloaded and unzipped [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data] from ArrayExpress website.
*#Specifically, [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw Data Zipped File]] (Found on team page).
**'''Basic steps to open expression data'''
*#Created New folder on desktop titled "dChip Analysis".
*#Unzipped folder by using 7zip "Unpack Here" option.
*#Placed .cdfin file in folder to run dChip.exe
*#Opened dChip software.
*#Clicked "Analysis"-->"Open Group".
*#Specified data directory as CEL file.
*#Selected working directory in "Options".
*#Selected following specifications and ran dChip:
*#[[Image: Other_information_dChip_screenshot.PNG]]
*#[[Image: Data_Files_dChip_Screenshot.PNG]]
*#[[Image: Options dChip screenshot.PNG]]
*#Select analysis--> Normalize and Model Data
*#Process each graph and hit "ok".
*#Tools-->"Export Expression Value"
*#Select all expression values-->run program-->find where file is saved.
*#Open file in .xls format-->name file "Master Spreadsheet".
**'''Renaming Columns in Master Spreadsheet'''
*#Access [[Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|sdrf file]] (found on team page).
*#Save link as.
*#Open using excel spreadsheet.
*#Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
*#Separate into 5 groups.
*#Find average of each group.
*#Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
*#Find EB to RB without rifampicin.
*#Find EB to RB with rifampicin.
*#Find Log Value (EB/RB) with/without rifampicin.
**'''Issues with Creating Master Excel Spreadsheet'''
*#Matched gene ID's from sdrf sheet to rename columns with meaningful titles.
*#Found that there were exactly 2 versions of every single gene ID in the raw data but not in the sdrf sheet.
*#Gene ID + Gene ID with "SE" at the end.
*#Found that "SE" denoted "standard error"
*#Deleted all duplicate "standard error" columns.
*#Could not do EB to RB with/without rifampicin for every rep. because there weren't matching files for every single rep.
*#Took Logbase 2 EB to RB for every rep. that had a matching rep. with/without rifampicin (=Log(Column1/Column2,2)).
*#Created new page in excel master sheet titled "EB to RB Values".
*#Copied all information from excel sheet where forumlae were ran to obtain data, pasted-->special-->values only.
*#Saved sheet as [[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]].

===Electronic Lab Notebook Week 13 (11/26/2013)===
*Met with Dahlquist during office hours.
*Created new excel spread sheet file with all of the raw data imported into one sheet named "dChip_2_signal1".
*Created new sheet and copy/pasted all of the raw data into the sheet and named it "edited_raw_data".
*Deleted all columns containing the P/A sequences as well as all the repeat "SE (standard error)" columns.
*Consulted sdrf file in order to find the EB/RB columns that did not contain rifampicin.
*Created new sheet titled "EB-to-RB".
*Copied all of the probe set data into column A.
*Copied all of the columns not containing rifampicin into columns B-G.
**EB was B-C. RB was D-G.
*Named column H "AverageEB" -- Found average of EB.
*Named column I "AverageRB" -- Found average of RB.
*Named column J "EB-to-RB" -- Took average of EB/Average of RB.
*Named column K "LogFC_EB-to-RB" -- Took log of EB to RB (column J).
**Formula: [=LOG(J2,2)]
*Named column L "P value".
**Ran ttest.
*Created new sheet named "EB-to-RB_Rifampicin".
*Saved file as [[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls|Master_Spreadsheet_Chlamydia_20131125_KD.xls]] found on team page.
*Following office hours, repeated process with the columns containing rifampicin.
*Saved file as [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] found on team page.

===Electronic Lab Notebook Week 15===
*Took initial [[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls |Master Spreadsheet Chlamydia V1 20131125 DW.xls]] spreadsheet and worked in conjunction with my group members to separate out the CTA and pCTA genes ID's to be tested in GenMAPP (see their respective pages for more information on the process by which they separated the gene ID's).
*Proceeded to take the genes for the CTA and pCTA and created a new sheet titled "For_GenMAPP".

[[Category:Journal Entry]]
[[Category:Individual Homework]]

Chlamydia trachomatis

2013-12-05T18:20:26Z

Dwilliams: /* Important Files */ Formatting

{{Team_H(oo)KD}}

==Deadlines and Intermediate Milestones==

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 8em; background: #ddd" | Monday
! style="width: 8em; background: #ddd" | Tuesday
! style="width: 8em; background: #ddd" | Wednesday
! style="width: 8em; background: #ddd" | Thursday
! style="width: 8em; background: #ddd" | Friday
|-
| style="vertical-align: top" | 11/11
| style="vertical-align: top" | 11/12
| style="vertical-align: top" | 11/13
| style="vertical-align: top" | 11/14
*Run an export/import of gene database cycle '''KS/HD'''
*Create species profile '''KS'''
*Obtain and format raw microarray data '''DW'''
| style="vertical-align: top" | 11/15
*Rerun export/import of gene database cycle '''KS'''
|-
| style="vertical-align: top; background: #eee" | 11/18
| style="vertical-align: top; background: #eee" | 11/19
*Vet the gene database exported last week '''KS/HD/DW'''
*Format the raw microarray data '''DW'''
| style="vertical-align: top; background: #eee" | 11/20
| style="vertical-align: top; background: #eee" | 11/21
*Perform microarray statistical analysis '''DW'''
*Work on custom species profile '''KS/HD'''
| style="vertical-align: top; background: #eee" | 11/22
|-
| style="vertical-align: top" | 11/25
| style="vertical-align: top" | 11/26
*Build and commit species profile '''KS'''
*Customize Tally Engine '''KS/HD'''
*Perform GenMAPP and MAPPFinder Analysis '''DW'''
| style="vertical-align: top" | 11/27
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/28
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/29
'''THANKSGIVING BREAK'''
|-
| style="vertical-align: top; background: #eee" | 12/02
| style="vertical-align: top; background: #eee" | 12/03
*Work on the final paper outline '''DW'''
*Document the relational database schema '''HD'''
*Commit changes to GenMAPP '''KS'''
| style="vertical-align: top; background: #eee" | 12/04
| style="vertical-align: top; background: #eee" | 12/05
*Begin writing the paper '''DW/KS/HD'''
*Begin working on the presentation '''DW/KS/HD'''
| style="vertical-align: top; background: #eee" | 12/06
|-
| style="vertical-align: top; background: #eee" | 12/09
| style="vertical-align: top; background: #eee" | 12/10
*Continue writing the paper '''HD/KS/DW'''
*Continue working on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/11
*Practice the final presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/12
*'''Final Presentation'''
*Proofread the final paper '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/13
|}

==Annotated Bibliography of Genomics Papers for ''C. trachomatis''==

===Whole genome sequencing of ''C. trachomatis''===

#Journal article describing results of whole genome sequencing:
#*Database: PubMed
#*Search Terms: Chlamydia trachomatis [MeSH Term] AND genome [Title]
#*There were 29 results. Many of the articles that appear using the above search terms have to do with performing whole-genome analysis of ''C. trachomatis'' to look at genetic polymorphisms in the bacterium and molecular and genetic characteristics that are observed when the bacterium infects a host.
#*Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R., Zhao, Q., Koonin, E. V., Davis, R.W. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. ''Science'' '''282''': 754-759. 10.1126/science.282.5389.754.
#*The article can be viewed as an [http://www.sciencemag.org/content/282/5389/754.long HTML].
#*The article can be viewed as a [[Media: Science-1998-Stephens-754-9.pdf | PDF]].
#*This article includes [http://www.sciencemag.org/site/feature/data/982604.xhtml Supplementary Material].
#Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
#*How many results did you get?: 872
#*Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?: Based on the titles and abstracts found in the results, it seems that research has been primarily in the direction of understanding how the disease functions and assessing the severity of the disease (and how to cure it).

===Microarray articles===
The EBI ArrayExpress database was used to locate each of the four following microarray articles. The search terms used were Chlamydia trachomatis under 'By organism' while the rest of the drop down menus were not altered.

The following articles appear in order of preference:

#Omsland, A., Sager, J., Nair, V., Sturdevant, D.E., Hackstadt, T. (2012) [http://www.pnas.org/content/109/48/19781.full Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]. ''PNAS'' '''109''': 19781-19785. doi: 10.1073/pnas.1212831109.
#*[[Media: PNAS-2012-Omsland-19781-5.pdf|PDF Version of Paper]]
#*[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data]
#*Chlamydiae undergo a biphasic developmental cycle characterized by an infectious cell type known as either an elementary body (EB) and an intracellular replicative form called a reticulate body (RB). Chlamydia was incubated under microaerobic conditions to test the differences in preferred energy source between EB's and RB's.
#*There weren't necessarily a "treatment" group and a "control" group. Referencing figure 4, it can be inferred that EB would be considered the "treatment" group because of the way that the ratio was set up, being EB to RB. In this way the RB would be the "control" group as they are looking at the EB population relative to the RB population.
#*4 Biological Replicates were performed for the control and treatment; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates...".


==Journal Club Presentation on ''C. trachomatis'' Genome Sequencing Paper==

[[Media:Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf|Here]] is the PDF version of the presentation given on November 12, 2013 on the Stephens ''et al.'' (1998) paper.


==Important Files==

*[[Media: Go_daily-termdb_v2_HD_20131107.obo-xml.gz|Go_daily-termdb_v2_HD_20131107.obo-xml.gz]]
:GO OBO-XML file for ''C. trachomatis'' serovar A.
*[[Media: Uniprot XML C.trachomatis serovar A KS 20131114.xml|Uniprot XML C.trachomatis serovar A KS 20131114.xml]]
:UniProt XML file for ''C. trachomatis'' serovar A.
*[[Media: 22183.C trachomatis A KS 20131114.goa|22183.C trachomatis A KS 20131114.goa]]
:GOA file for ''C. trachomatis'' serovar A.
*[[Media: Ct-Std v1 KS 20131119.gdb|Ct-Std v1 KS 20131119.gdb]]
:First iteration of the export/import gene database cycle.
*[[Media: Ct-Std KS 20131121.gdb|Ct-Std KS 20131121.gdb]]
:Updated gene database.
*[[Media: Ct-Std v2 KS 20131121.gdb|Ct-Std v2 KS 20131121.gdb]]
:New gene database created with the new version of gmbuilder built on 11/21/2013 using the custom species profile for ''C. trachomatis.''

'''Array Express Article Raw Files'''

*[[Media:Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt|Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt]]
:Microarray raw ADF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt]]
:Microarray raw IDF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip]]
:Microarray raw processed zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip]]
:Microarray raw zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt]]
:Microarray SDRF text file for ''C. trachomatis''.
*[[Media:Sdrf information excel.xls|Sdrf information excel.xls]]
:sdrf information in excel spreadsheet format.

'''Excel Master Spreadsheet File Versions (Containing the Formatted Raw Data)'''

*[[Media:Master Spreadsheet.xls|master spreadsheet work in progress]]
:Initial Microarray raw data formatted and opened in Microsoft Excel.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls]]
:Sample C. trachomatis microarray data that was used to run GenMAPP with the latest ''C. trachomatis'' database.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt]]
:Tab-delimited version of the file above.
*[[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]]
:Microarray data with identified Gene ID's and Log base data.
*[[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls | Master_Spreadsheet_Chlamydia_20131125_KD.xls]]
:version edited during office hours by Dr. Dahlquist to demonstrate statistics
*[[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls]]
:finished version of version edited during office hours by Dr. Dahlquist to demonstrate statistics -- finished by Dillon Williams
*[[Media: Copy of Master Spreadsheet Chlamydia V2 20131203 HD.xls]]
:Microarray data with separated IDs CTA_#### from _RRMH#####_...
*[[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]]
:Excel Speadsheet with data formatted for GenMAPP (Version run in GenMAPP).

'''For GenMAPP Files'''
*[[Media: Ctrachomatis EbtoRb ATP metabolic process.mapp]]
: EB to RB ATP Metabolic Process Mapp file.
*[[Media: Ctrachomatis EbtoRB glucose catabolic process 20131204 DW.mapp]]
: EB to RB glucose catabolic process map.
*[[Media: CTrachomatis EBtoRB Rifampicin 20131204 DW-Criterion1-GO.txt]]
: EB to RB Rifampicin go.txt file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.gex]]
: For_GenMAPP .gex file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.gmf]]
: For GenMAPP .gmf file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.zip]]
: Access file created with .gex file.

==Wiki Formatting==

Template: [[Template:Team_H(oo)KD]]

[[Category: Group Projects]]
[[Category: Team H(oo)KD]]

Chlamydia trachomatis

2013-12-05T18:15:27Z

Dwilliams: /* Important Files */ Fixed some links

{{Team_H(oo)KD}}

==Deadlines and Intermediate Milestones==

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 8em; background: #ddd" | Monday
! style="width: 8em; background: #ddd" | Tuesday
! style="width: 8em; background: #ddd" | Wednesday
! style="width: 8em; background: #ddd" | Thursday
! style="width: 8em; background: #ddd" | Friday
|-
| style="vertical-align: top" | 11/11
| style="vertical-align: top" | 11/12
| style="vertical-align: top" | 11/13
| style="vertical-align: top" | 11/14
*Run an export/import of gene database cycle '''KS/HD'''
*Create species profile '''KS'''
*Obtain and format raw microarray data '''DW'''
| style="vertical-align: top" | 11/15
*Rerun export/import of gene database cycle '''KS'''
|-
| style="vertical-align: top; background: #eee" | 11/18
| style="vertical-align: top; background: #eee" | 11/19
*Vet the gene database exported last week '''KS/HD/DW'''
*Format the raw microarray data '''DW'''
| style="vertical-align: top; background: #eee" | 11/20
| style="vertical-align: top; background: #eee" | 11/21
*Perform microarray statistical analysis '''DW'''
*Work on custom species profile '''KS/HD'''
| style="vertical-align: top; background: #eee" | 11/22
|-
| style="vertical-align: top" | 11/25
| style="vertical-align: top" | 11/26
*Build and commit species profile '''KS'''
*Customize Tally Engine '''KS/HD'''
*Perform GenMAPP and MAPPFinder Analysis '''DW'''
| style="vertical-align: top" | 11/27
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/28
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/29
'''THANKSGIVING BREAK'''
|-
| style="vertical-align: top; background: #eee" | 12/02
| style="vertical-align: top; background: #eee" | 12/03
*Work on the final paper outline '''DW'''
*Document the relational database schema '''HD'''
*Commit changes to GenMAPP '''KS'''
| style="vertical-align: top; background: #eee" | 12/04
| style="vertical-align: top; background: #eee" | 12/05
*Begin writing the paper '''DW/KS/HD'''
*Begin working on the presentation '''DW/KS/HD'''
| style="vertical-align: top; background: #eee" | 12/06
|-
| style="vertical-align: top; background: #eee" | 12/09
| style="vertical-align: top; background: #eee" | 12/10
*Continue writing the paper '''HD/KS/DW'''
*Continue working on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/11
*Practice the final presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/12
*'''Final Presentation'''
*Proofread the final paper '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/13
|}

==Annotated Bibliography of Genomics Papers for ''C. trachomatis''==

===Whole genome sequencing of ''C. trachomatis''===

#Journal article describing results of whole genome sequencing:
#*Database: PubMed
#*Search Terms: Chlamydia trachomatis [MeSH Term] AND genome [Title]
#*There were 29 results. Many of the articles that appear using the above search terms have to do with performing whole-genome analysis of ''C. trachomatis'' to look at genetic polymorphisms in the bacterium and molecular and genetic characteristics that are observed when the bacterium infects a host.
#*Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R., Zhao, Q., Koonin, E. V., Davis, R.W. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. ''Science'' '''282''': 754-759. 10.1126/science.282.5389.754.
#*The article can be viewed as an [http://www.sciencemag.org/content/282/5389/754.long HTML].
#*The article can be viewed as a [[Media: Science-1998-Stephens-754-9.pdf | PDF]].
#*This article includes [http://www.sciencemag.org/site/feature/data/982604.xhtml Supplementary Material].
#Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
#*How many results did you get?: 872
#*Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?: Based on the titles and abstracts found in the results, it seems that research has been primarily in the direction of understanding how the disease functions and assessing the severity of the disease (and how to cure it).

===Microarray articles===
The EBI ArrayExpress database was used to locate each of the four following microarray articles. The search terms used were Chlamydia trachomatis under 'By organism' while the rest of the drop down menus were not altered.

The following articles appear in order of preference:

#Omsland, A., Sager, J., Nair, V., Sturdevant, D.E., Hackstadt, T. (2012) [http://www.pnas.org/content/109/48/19781.full Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]. ''PNAS'' '''109''': 19781-19785. doi: 10.1073/pnas.1212831109.
#*[[Media: PNAS-2012-Omsland-19781-5.pdf|PDF Version of Paper]]
#*[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data]
#*Chlamydiae undergo a biphasic developmental cycle characterized by an infectious cell type known as either an elementary body (EB) and an intracellular replicative form called a reticulate body (RB). Chlamydia was incubated under microaerobic conditions to test the differences in preferred energy source between EB's and RB's.
#*There weren't necessarily a "treatment" group and a "control" group. Referencing figure 4, it can be inferred that EB would be considered the "treatment" group because of the way that the ratio was set up, being EB to RB. In this way the RB would be the "control" group as they are looking at the EB population relative to the RB population.
#*4 Biological Replicates were performed for the control and treatment; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates...".


==Journal Club Presentation on ''C. trachomatis'' Genome Sequencing Paper==

[[Media:Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf|Here]] is the PDF version of the presentation given on November 12, 2013 on the Stephens ''et al.'' (1998) paper.


==Important Files==

*[[Media: Go_daily-termdb_v2_HD_20131107.obo-xml.gz|Go_daily-termdb_v2_HD_20131107.obo-xml.gz]]
:GO OBO-XML file for ''C. trachomatis'' serovar A.
*[[Media: Uniprot XML C.trachomatis serovar A KS 20131114.xml|Uniprot XML C.trachomatis serovar A KS 20131114.xml]]
:UniProt XML file for ''C. trachomatis'' serovar A.
*[[Media: 22183.C trachomatis A KS 20131114.goa|22183.C trachomatis A KS 20131114.goa]]
:GOA file for ''C. trachomatis'' serovar A.
*[[Media: Ct-Std v1 KS 20131119.gdb|Ct-Std v1 KS 20131119.gdb]]
:First iteration of the export/import gene database cycle.
*[[Media: Ct-Std KS 20131121.gdb|Ct-Std KS 20131121.gdb]]
:Updated gene database.
*[[Media: Ct-Std v2 KS 20131121.gdb|Ct-Std v2 KS 20131121.gdb]]
:New gene database created with the new version of gmbuilder built on 11/21/2013 using the custom species profile for ''C. trachomatis.''

'''Array Express Article Raw Files'''

*[[Media:Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt|Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt]]
:Microarray raw ADF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt]]
:Microarray raw IDF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip]]
:Microarray raw processed zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip]]
:Microarray raw zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt]]
:Microarray SDRF text file for ''C. trachomatis''.
*[[Media:Sdrf information excel.xls|Sdrf information excel.xls]]
:sdrf information in excel spreadsheet format.

'''Excel Master Spreadsheet Files (Containing the Formatted Raw Data)'''

*[[Media:Master Spreadsheet.xls|master spreadsheet work in progress]]
:Initial Microarray raw data formatted and opened in Microsoft Excel.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls]]
:Sample C. trachomatis microarray data that was used to run GenMAPP with the latest ''C. trachomatis'' database.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt]]
:Tab-delimited version of the file above.
*[[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]]
:Microarray data with identified Gene ID's and Log base data.
*[[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls | Master_Spreadsheet_Chlamydia_20131125_KD.xls]]
:version edited during office hours by Dr. Dahlquist to demonstrate statistics
*[[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls]]
:finished version of version edited during office hours by Dr. Dahlquist to demonstrate statistics -- finished by Dillon Williams
*[[Media: Copy of Master Spreadsheet Chlamydia V2 20131203 HD.xls]]
:Microarray data with separated IDs CTA_#### from _RRMH#####_...
*[[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]]
:Excel Speadsheet with data formatted for GenMAPP (Version run in GenMAPP).

'''For GenMAPP Files'''
*[[Media: Ctrachomatis EbtoRb ATP metabolic process.mapp]]
: EB to RB ATP Metabolic Process Mapp file.
*[[Media: Ctrachomatis EbtoRB glucose catabolic process 20131204 DW.mapp]]
: EB to RB glucose catabolic process map.
*[[Media: CTrachomatis EBtoRB Rifampicin 20131204 DW-Criterion1-GO.txt]]
: EB to RB Rifampicin go.txt file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.gex]]
: For_GenMAPP .gex file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.gmf]]
: For GenMAPP .gmf file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.zip]]
: Access file created with .gex file.

==Wiki Formatting==

Template: [[Template:Team_H(oo)KD]]

[[Category: Group Projects]]
[[Category: Team H(oo)KD]]

Chlamydia trachomatis

2013-12-05T18:15:04Z

Dwilliams: /* Important Files */ Added all "for genmapp" files

{{Team_H(oo)KD}}

==Deadlines and Intermediate Milestones==

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 8em; background: #ddd" | Monday
! style="width: 8em; background: #ddd" | Tuesday
! style="width: 8em; background: #ddd" | Wednesday
! style="width: 8em; background: #ddd" | Thursday
! style="width: 8em; background: #ddd" | Friday
|-
| style="vertical-align: top" | 11/11
| style="vertical-align: top" | 11/12
| style="vertical-align: top" | 11/13
| style="vertical-align: top" | 11/14
*Run an export/import of gene database cycle '''KS/HD'''
*Create species profile '''KS'''
*Obtain and format raw microarray data '''DW'''
| style="vertical-align: top" | 11/15
*Rerun export/import of gene database cycle '''KS'''
|-
| style="vertical-align: top; background: #eee" | 11/18
| style="vertical-align: top; background: #eee" | 11/19
*Vet the gene database exported last week '''KS/HD/DW'''
*Format the raw microarray data '''DW'''
| style="vertical-align: top; background: #eee" | 11/20
| style="vertical-align: top; background: #eee" | 11/21
*Perform microarray statistical analysis '''DW'''
*Work on custom species profile '''KS/HD'''
| style="vertical-align: top; background: #eee" | 11/22
|-
| style="vertical-align: top" | 11/25
| style="vertical-align: top" | 11/26
*Build and commit species profile '''KS'''
*Customize Tally Engine '''KS/HD'''
*Perform GenMAPP and MAPPFinder Analysis '''DW'''
| style="vertical-align: top" | 11/27
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/28
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/29
'''THANKSGIVING BREAK'''
|-
| style="vertical-align: top; background: #eee" | 12/02
| style="vertical-align: top; background: #eee" | 12/03
*Work on the final paper outline '''DW'''
*Document the relational database schema '''HD'''
*Commit changes to GenMAPP '''KS'''
| style="vertical-align: top; background: #eee" | 12/04
| style="vertical-align: top; background: #eee" | 12/05
*Begin writing the paper '''DW/KS/HD'''
*Begin working on the presentation '''DW/KS/HD'''
| style="vertical-align: top; background: #eee" | 12/06
|-
| style="vertical-align: top; background: #eee" | 12/09
| style="vertical-align: top; background: #eee" | 12/10
*Continue writing the paper '''HD/KS/DW'''
*Continue working on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/11
*Practice the final presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/12
*'''Final Presentation'''
*Proofread the final paper '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/13
|}

==Annotated Bibliography of Genomics Papers for ''C. trachomatis''==

===Whole genome sequencing of ''C. trachomatis''===

#Journal article describing results of whole genome sequencing:
#*Database: PubMed
#*Search Terms: Chlamydia trachomatis [MeSH Term] AND genome [Title]
#*There were 29 results. Many of the articles that appear using the above search terms have to do with performing whole-genome analysis of ''C. trachomatis'' to look at genetic polymorphisms in the bacterium and molecular and genetic characteristics that are observed when the bacterium infects a host.
#*Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R., Zhao, Q., Koonin, E. V., Davis, R.W. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. ''Science'' '''282''': 754-759. 10.1126/science.282.5389.754.
#*The article can be viewed as an [http://www.sciencemag.org/content/282/5389/754.long HTML].
#*The article can be viewed as a [[Media: Science-1998-Stephens-754-9.pdf | PDF]].
#*This article includes [http://www.sciencemag.org/site/feature/data/982604.xhtml Supplementary Material].
#Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
#*How many results did you get?: 872
#*Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?: Based on the titles and abstracts found in the results, it seems that research has been primarily in the direction of understanding how the disease functions and assessing the severity of the disease (and how to cure it).

===Microarray articles===
The EBI ArrayExpress database was used to locate each of the four following microarray articles. The search terms used were Chlamydia trachomatis under 'By organism' while the rest of the drop down menus were not altered.

The following articles appear in order of preference:

#Omsland, A., Sager, J., Nair, V., Sturdevant, D.E., Hackstadt, T. (2012) [http://www.pnas.org/content/109/48/19781.full Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]. ''PNAS'' '''109''': 19781-19785. doi: 10.1073/pnas.1212831109.
#*[[Media: PNAS-2012-Omsland-19781-5.pdf|PDF Version of Paper]]
#*[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data]
#*Chlamydiae undergo a biphasic developmental cycle characterized by an infectious cell type known as either an elementary body (EB) and an intracellular replicative form called a reticulate body (RB). Chlamydia was incubated under microaerobic conditions to test the differences in preferred energy source between EB's and RB's.
#*There weren't necessarily a "treatment" group and a "control" group. Referencing figure 4, it can be inferred that EB would be considered the "treatment" group because of the way that the ratio was set up, being EB to RB. In this way the RB would be the "control" group as they are looking at the EB population relative to the RB population.
#*4 Biological Replicates were performed for the control and treatment; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates...".


==Journal Club Presentation on ''C. trachomatis'' Genome Sequencing Paper==

[[Media:Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf|Here]] is the PDF version of the presentation given on November 12, 2013 on the Stephens ''et al.'' (1998) paper.


==Important Files==

*[[Media: Go_daily-termdb_v2_HD_20131107.obo-xml.gz|Go_daily-termdb_v2_HD_20131107.obo-xml.gz]]
:GO OBO-XML file for ''C. trachomatis'' serovar A.
*[[Media: Uniprot XML C.trachomatis serovar A KS 20131114.xml|Uniprot XML C.trachomatis serovar A KS 20131114.xml]]
:UniProt XML file for ''C. trachomatis'' serovar A.
*[[Media: 22183.C trachomatis A KS 20131114.goa|22183.C trachomatis A KS 20131114.goa]]
:GOA file for ''C. trachomatis'' serovar A.
*[[Media: Ct-Std v1 KS 20131119.gdb|Ct-Std v1 KS 20131119.gdb]]
:First iteration of the export/import gene database cycle.
*[[Media: Ct-Std KS 20131121.gdb|Ct-Std KS 20131121.gdb]]
:Updated gene database.
*[[Media: Ct-Std v2 KS 20131121.gdb|Ct-Std v2 KS 20131121.gdb]]
:New gene database created with the new version of gmbuilder built on 11/21/2013 using the custom species profile for ''C. trachomatis.''

'''Array Express Article Raw Files'''

*[[Media:Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt|Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt]]
:Microarray raw ADF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt]]
:Microarray raw IDF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip]]
:Microarray raw processed zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip]]
:Microarray raw zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt]]
:Microarray SDRF text file for ''C. trachomatis''.
*[[Media:Sdrf information excel.xls|Sdrf information excel.xls]]
:sdrf information in excel spreadsheet format.

'''Excel Master Spreadsheet Files (Containing the Formatted Raw Data)'''

*[[Media:Master Spreadsheet.xls|master spreadsheet work in progress]]
:Initial Microarray raw data formatted and opened in Microsoft Excel.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls]]
:Sample C. trachomatis microarray data that was used to run GenMAPP with the latest ''C. trachomatis'' database.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt]]
:Tab-delimited version of the file above.
*[[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]]
:Microarray data with identified Gene ID's and Log base data.
*[[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls | Master_Spreadsheet_Chlamydia_20131125_KD.xls]]
:version edited during office hours by Dr. Dahlquist to demonstrate statistics
*[[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls]]
:finished version of version edited during office hours by Dr. Dahlquist to demonstrate statistics -- finished by Dillon Williams
*[[Media: Copy of Master Spreadsheet Chlamydia V2 20131203 HD.xls]]
:Microarray data with separated IDs CTA_#### from _RRMH#####_...
*[[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]]
:Excel Speadsheet with data formatted for GenMAPP (Version run in GenMAPP).

'''For GenMAPP Files'''
*[[Media: Ctrachomatis EbtoRb ATP metabolic process.mapp]]
: EB to RB ATP Metabolic Process Mapp file.
*[[Media: Ctrachomatis EbtoRB glucose catabolic process 20131204 DW.mapp]]
: EB to RB glucose catabolic process map.
*[[Meida: CTrachomatis EBtoRB Rifampicin 20131204 DW-Criterion1-GO.txt]]
: EB to RB Rifampicin go.txt file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.gex]]
: For_GenMAPP .gex file.
*[[Meida: For GenMAPP Chlamydia V4 20131204 KS.gmf]]
: For GenMAPP .gmf file.
*[[Media: For GenMAPP Chlamydia V4 20131204 KS.zip]]
: Access file created with .gex file.

==Wiki Formatting==

Template: [[Template:Team_H(oo)KD]]

[[Category: Group Projects]]
[[Category: Team H(oo)KD]]

Chlamydia trachomatis

2013-12-05T18:11:34Z

Dwilliams: /* Important Files */

{{Team_H(oo)KD}}

==Deadlines and Intermediate Milestones==

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 8em; background: #ddd" | Monday
! style="width: 8em; background: #ddd" | Tuesday
! style="width: 8em; background: #ddd" | Wednesday
! style="width: 8em; background: #ddd" | Thursday
! style="width: 8em; background: #ddd" | Friday
|-
| style="vertical-align: top" | 11/11
| style="vertical-align: top" | 11/12
| style="vertical-align: top" | 11/13
| style="vertical-align: top" | 11/14
*Run an export/import of gene database cycle '''KS/HD'''
*Create species profile '''KS'''
*Obtain and format raw microarray data '''DW'''
| style="vertical-align: top" | 11/15
*Rerun export/import of gene database cycle '''KS'''
|-
| style="vertical-align: top; background: #eee" | 11/18
| style="vertical-align: top; background: #eee" | 11/19
*Vet the gene database exported last week '''KS/HD/DW'''
*Format the raw microarray data '''DW'''
| style="vertical-align: top; background: #eee" | 11/20
| style="vertical-align: top; background: #eee" | 11/21
*Perform microarray statistical analysis '''DW'''
*Work on custom species profile '''KS/HD'''
| style="vertical-align: top; background: #eee" | 11/22
|-
| style="vertical-align: top" | 11/25
| style="vertical-align: top" | 11/26
*Build and commit species profile '''KS'''
*Customize Tally Engine '''KS/HD'''
*Perform GenMAPP and MAPPFinder Analysis '''DW'''
| style="vertical-align: top" | 11/27
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/28
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/29
'''THANKSGIVING BREAK'''
|-
| style="vertical-align: top; background: #eee" | 12/02
| style="vertical-align: top; background: #eee" | 12/03
*Work on the final paper outline '''DW'''
*Document the relational database schema '''HD'''
*Commit changes to GenMAPP '''KS'''
| style="vertical-align: top; background: #eee" | 12/04
| style="vertical-align: top; background: #eee" | 12/05
*Begin writing the paper '''DW/KS/HD'''
*Begin working on the presentation '''DW/KS/HD'''
| style="vertical-align: top; background: #eee" | 12/06
|-
| style="vertical-align: top; background: #eee" | 12/09
| style="vertical-align: top; background: #eee" | 12/10
*Continue writing the paper '''HD/KS/DW'''
*Continue working on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/11
*Practice the final presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/12
*'''Final Presentation'''
*Proofread the final paper '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/13
|}

==Annotated Bibliography of Genomics Papers for ''C. trachomatis''==

===Whole genome sequencing of ''C. trachomatis''===

#Journal article describing results of whole genome sequencing:
#*Database: PubMed
#*Search Terms: Chlamydia trachomatis [MeSH Term] AND genome [Title]
#*There were 29 results. Many of the articles that appear using the above search terms have to do with performing whole-genome analysis of ''C. trachomatis'' to look at genetic polymorphisms in the bacterium and molecular and genetic characteristics that are observed when the bacterium infects a host.
#*Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R., Zhao, Q., Koonin, E. V., Davis, R.W. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. ''Science'' '''282''': 754-759. 10.1126/science.282.5389.754.
#*The article can be viewed as an [http://www.sciencemag.org/content/282/5389/754.long HTML].
#*The article can be viewed as a [[Media: Science-1998-Stephens-754-9.pdf | PDF]].
#*This article includes [http://www.sciencemag.org/site/feature/data/982604.xhtml Supplementary Material].
#Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
#*How many results did you get?: 872
#*Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?: Based on the titles and abstracts found in the results, it seems that research has been primarily in the direction of understanding how the disease functions and assessing the severity of the disease (and how to cure it).

===Microarray articles===
The EBI ArrayExpress database was used to locate each of the four following microarray articles. The search terms used were Chlamydia trachomatis under 'By organism' while the rest of the drop down menus were not altered.

The following articles appear in order of preference:

#Omsland, A., Sager, J., Nair, V., Sturdevant, D.E., Hackstadt, T. (2012) [http://www.pnas.org/content/109/48/19781.full Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]. ''PNAS'' '''109''': 19781-19785. doi: 10.1073/pnas.1212831109.
#*[[Media: PNAS-2012-Omsland-19781-5.pdf|PDF Version of Paper]]
#*[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data]
#*Chlamydiae undergo a biphasic developmental cycle characterized by an infectious cell type known as either an elementary body (EB) and an intracellular replicative form called a reticulate body (RB). Chlamydia was incubated under microaerobic conditions to test the differences in preferred energy source between EB's and RB's.
#*There weren't necessarily a "treatment" group and a "control" group. Referencing figure 4, it can be inferred that EB would be considered the "treatment" group because of the way that the ratio was set up, being EB to RB. In this way the RB would be the "control" group as they are looking at the EB population relative to the RB population.
#*4 Biological Replicates were performed for the control and treatment; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates...".


==Journal Club Presentation on ''C. trachomatis'' Genome Sequencing Paper==

[[Media:Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf|Here]] is the PDF version of the presentation given on November 12, 2013 on the Stephens ''et al.'' (1998) paper.


==Important Files==

*[[Media: Go_daily-termdb_v2_HD_20131107.obo-xml.gz|Go_daily-termdb_v2_HD_20131107.obo-xml.gz]]
:GO OBO-XML file for ''C. trachomatis'' serovar A.
*[[Media: Uniprot XML C.trachomatis serovar A KS 20131114.xml|Uniprot XML C.trachomatis serovar A KS 20131114.xml]]
:UniProt XML file for ''C. trachomatis'' serovar A.
*[[Media: 22183.C trachomatis A KS 20131114.goa|22183.C trachomatis A KS 20131114.goa]]
:GOA file for ''C. trachomatis'' serovar A.
*[[Media: Ct-Std v1 KS 20131119.gdb|Ct-Std v1 KS 20131119.gdb]]
:First iteration of the export/import gene database cycle.
*[[Media: Ct-Std KS 20131121.gdb|Ct-Std KS 20131121.gdb]]
:Updated gene database.
*[[Media: Ct-Std v2 KS 20131121.gdb|Ct-Std v2 KS 20131121.gdb]]
:New gene database created with the new version of gmbuilder built on 11/21/2013 using the custom species profile for ''C. trachomatis.''

'''Array Express Article Raw Files'''

*[[Media:Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt|Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt]]
:Microarray raw ADF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt]]
:Microarray raw IDF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip]]
:Microarray raw processed zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip]]
:Microarray raw zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt]]
:Microarray SDRF text file for ''C. trachomatis''.
*[[Media:Sdrf information excel.xls|Sdrf information excel.xls]]
:sdrf information in excel spreadsheet format.

'''Excel Master Spreadsheet Files (Containing the Formatted Raw Data)'''

*[[Media:Master Spreadsheet.xls|master spreadsheet work in progress]]
:Initial Microarray raw data formatted and opened in Microsoft Excel.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls]]
:Sample C. trachomatis microarray data that was used to run GenMAPP with the latest ''C. trachomatis'' database.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt]]
:Tab-delimited version of the file above.
*[[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]]
:Microarray data with identified Gene ID's and Log base data.
*[[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls | Master_Spreadsheet_Chlamydia_20131125_KD.xls]]
:version edited during office hours by Dr. Dahlquist to demonstrate statistics
*[[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls]]
:finished version of version edited during office hours by Dr. Dahlquist to demonstrate statistics -- finished by Dillon Williams
*[[Media: Copy of Master Spreadsheet Chlamydia V2 20131203 HD.xls]]
:Microarray data with separated IDs CTA_#### from _RRMH#####_...
*[[Media: For GenMAPP Chlamydia V4 20131203 DW.xls]]
:Excel Speadsheet with data formatted for GenMAPP (Version run in GenMAPP).

'''For GenMAPP Files'''

==Wiki Formatting==

Template: [[Template:Team_H(oo)KD]]

[[Category: Group Projects]]
[[Category: Team H(oo)KD]]

File:For GenMAPP Chlamydia V4 20131204 KS.zip

2013-12-05T18:10:31Z

Dwilliams: Access file created with .gex file

Access file created with .gex file

File:For GenMAPP Chlamydia V4 20131204 KS.gmf

2013-12-05T18:07:59Z

Dwilliams: For GenMAPP .gmf file

For GenMAPP .gmf file

File:For GenMAPP Chlamydia V4 20131204 KS.gex

2013-12-05T18:07:18Z

Dwilliams: For_GenMAPP .gex file

For_GenMAPP .gex file

File:CTrachomatis EBtoRB Rifampicin 20131204 DW-Criterion1-GO.txt

2013-12-05T18:06:52Z

Dwilliams: EB to RB Rifampicin go.txt file

EB to RB Rifampicin go.txt file