Difference between revisions of "Chlamydia trachomatis"

From LMU BioDB 2013
Jump to: navigation, search
(→‎Microarray articles: Added information about the treatment and control groups in the Carlson et al. paper)
(→‎Important Files: Formatting)
 
(111 intermediate revisions by 4 users not shown)
Line 1: Line 1:
−
'''Team H(oo)KD:'''
+
{{Team_H(oo)KD}}
−
*Quality Assurance: [[User:HDelgadi|Hilda Delgadillo]]
+
 
−
*Coder: [[User:Ksherbina|Katrina Sherbina]]
+
==Deadlines and Intermediate Milestones==
−
*GenMAPP User: [[User:Dwilliams|Dillon Williams]]
+
 
 +
{| 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''==
 
==Annotated Bibliography of Genomics Papers for ''C. trachomatis''==
Line 11: Line 112:
 
#*Database: PubMed
 
#*Database: PubMed
 
#*Search Terms: Chlamydia trachomatis [MeSH Term] AND genome [Title]
 
#*Search Terms: Chlamydia trachomatis [MeSH Term] AND genome [Title]
−
#*Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L.,... Davis, R.W. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. ''Science'' '''282''': 754-759.
+
#*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.
 
#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
 
#*How many results did you get?: 872
Line 18: Line 123:
 
===Microarray articles===  
 
===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 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...".
 +
<!--
 
#Song L, Carlson JH, Whitmire WM, Kari L et al. [http://iai.asm.org/content/81/3/636.long Chlamydia trachomatis plasmid-encoded Pgp4 is a transcriptional regulator of virulence-associated genes.] Infect Immun 2013 Mar;81(3):636-44.
 
#Song L, Carlson JH, Whitmire WM, Kari L et al. [http://iai.asm.org/content/81/3/636.long Chlamydia trachomatis plasmid-encoded Pgp4 is a transcriptional regulator of virulence-associated genes.] Infect Immun 2013 Mar;81(3):636-44.
−
#*
+
#*The experiment performed consisted of looking at Chlamydia's plasmid which is significantly importance towards Chlamydia's virulence. Through the experiment, the eight open reading frames within the plasmid were deleted one by one in order to better understand the function and importance of the plasmid in terms of its relationship to Chlamydia's virulence. Ultimately, it was found that the Pgp4 Open Reading Frame functions as a transcriptional regulator of the glycogen synthase gene glgA, that is likely responsible for Chlamydia's pathogenic nature.
 +
#*The treatment was the plasmid infected with L2, L2R, L2Rp+, L2RpΔpgp4, or L2RpΔpgp5 and six replicates were made for each infected group. The control was the mock infected plasmid and six replicates were made for the control.
 +
#*The technical replicates for each treatment and control group were six of each.
 +
#*[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40979/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data]
 
#Carlson JH, Whitmire WM, Crane DD, Wicke L et al. [http://iai.asm.org/content/76/6/2273.long The Chlamydia trachomatis plasmid is a transcriptional regulator of chromosomal genes and a virulence factor.] Infect Immun 2008 Jun;76(6):2273-83.  
 
#Carlson JH, Whitmire WM, Crane DD, Wicke L et al. [http://iai.asm.org/content/76/6/2273.long The Chlamydia trachomatis plasmid is a transcriptional regulator of chromosomal genes and a virulence factor.] Infect Immun 2008 Jun;76(6):2273-83.  
 
#*Different types of molecular and transcriptomic analyses were performed for two strains of ''Chlamydia trachomatis'', specifically the plasmidless strain L2(25667R) and the plasmid-positive strain L2(434), to determine the function of the 7.5-kb plasmid in the bacterium.  
 
#*Different types of molecular and transcriptomic analyses were performed for two strains of ''Chlamydia trachomatis'', specifically the plasmidless strain L2(25667R) and the plasmid-positive strain L2(434), to determine the function of the 7.5-kb plasmid in the bacterium.  
 
#*There were two treatment groups: McCoy cells (4 × 107 cells) infected with L2(434) and McCoy cells L2(25667R). The control group was mock infected McCoy cells.
 
#*There were two treatment groups: McCoy cells (4 × 107 cells) infected with L2(434) and McCoy cells L2(25667R). The control group was mock infected McCoy cells.
−
#Omsland A, Sager J, Nair V, Sturdevant DE, Hackstadt T. , et al. [http://www.pnas.org/content/109/48/19781.full#sec-10 Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]
+
#*There were 6 technical replicates for the control group and each of the treatment groups.
−
#*Selected article: [[http://www.pnas.org/content/109/48/19781.full Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]]
+
#*[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-10199/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray data]
−
#*[[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.
+
*NOTE: Dillon looked at the Omsland et al. paper, Hilda looked at the Song et al. paper, and Katrina looked at the Carlson et al. paper.
−
#*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.
+
-->
−
#*Replicates were performed for the control and treatment in terms of technical replicates; 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.
 +
<!--
 +
#Opted for paper suggested by professor Dahlquist in post-assignment discussion:
 +
#*[http://iai.asm.org/content/73/10/6407.long Carlson, J.H. et al. (2005) Comparative Genomic Analysis of Chlamydia trachomatis Oculotropic and Genitotropic Strains Infect. Immun. 73: 6407-6418.]
 +
#*[[Media: Infect._Immun.-2005-Carlson-6407-18.pdf|PDF Version of Genome 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]]
  
−
#What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
+
[[Category: Group Projects]]
−
#Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
+
[[Category: Team H(oo)KD]]
−
#What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
+
−
#Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
+

Latest revision as of 23:36, 13 December 2013

Team H(oo)KD
Project Manager/Coder: Katrina Sherbina Quality Assurance: Hilda Delgadillo GenMAPP User: Dillon Williams
Project Guidelines: Gene Database Project Report Guidelines
Team Journal Assignments Week 12 Status Report Week 13 Status Report Week 15 Status Report
Individual Status Reports: HDelgadi Project Notebook dwilliams Project Notebook Ksherbina Project Notebook
Useful Links: Class Page Team Home Page
Final Product Project Deliverables

Contents

[edit] Deadlines and Intermediate Milestones

Monday Tuesday Wednesday Thursday Friday
11/11 11/12 11/13 11/14
  • Run an export/import of gene database cycle KS/HD
  • Create species profile KS
  • Obtain and format raw microarray data DW
11/15
  • Rerun export/import of gene database cycle KS
11/18 11/19
  • Vet the gene database exported last week KS/HD/DW
  • Format the raw microarray data DW
11/20 11/21
  • Perform microarray statistical analysis DW
  • Work on custom species profile KS/HD
11/22
11/25 11/26
  • Build and commit species profile KS
  • Customize Tally Engine KS/HD
  • Perform GenMAPP and MAPPFinder Analysis DW
11/27

THANKSGIVING BREAK

11/28

THANKSGIVING BREAK

11/29

THANKSGIVING BREAK

12/02 12/03
  • Run GenMAPP and MAPPFinder DW
  • Customize the Tally Engine for C. trachomatis DW
12/04
  • Run GenMAPP and MAPPFinder again if necessary DW
12/05
  • Begin working on the relational database schema HD
  • Commit the changes to gmbuilder KS
12/06
12/09
  • Write the paper HD/KS/DW
  • Work on the presentation HD/KS/DW
12/10
  • Write the paper HD/KS/DW
  • Work on the presentation HD/KS/DW
12/11
  • Finish the presentation HD/KS/DW
  • Practice the final presentation HD/KS/DW
12/12
  • Final Presentation
  • Proofread the final paper HD/KS/DW
  • Make sure all the deliverables are raedy HD/KS/DW
12/13

[edit] Deliverable and Final Paper Assignments

[edit] 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

[edit] Final Paper

  1. Introduction Hilda
  2. 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
  3. 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
  4. 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

[edit] Annotated Bibliography of Genomics Papers for C. trachomatis

[edit] Whole genome sequencing of C. trachomatis

  1. 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 HTML.
    • The article can be viewed as a PDF.
    • This article includes Supplementary Material.
  2. 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).

[edit] 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:

  1. Omsland, A., Sager, J., Nair, V., Sturdevant, D.E., Hackstadt, T. (2012) Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium. PNAS 109: 19781-19785. doi: 10.1073/pnas.1212831109.
    • PDF Version of Paper
    • 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...".

[edit] Journal Club Presentation on C. trachomatis Genome Sequencing Paper

Here is the PDF version of the presentation given on November 12, 2013 on the Stephens et al. (1998) paper.

[edit] Important Files

GO OBO-XML file for C. trachomatis serovar A.
UniProt XML file for C. trachomatis serovar A.
GOA file for C. trachomatis serovar A.
First iteration of the export/import gene database cycle.
Updated gene database.
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

Microarray raw ADF file for C. trachomatis.
Microarray raw IDF file for C. trachomatis.
Microarray raw processed zip file for C. trachomatis.
Microarray raw zip file for C. trachomatis.
Microarray SDRF text file for C. trachomatis.
sdrf information in excel spreadsheet format.

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

Initial Microarray raw data formatted and opened in Microsoft Excel.
Sample C. trachomatis microarray data that was used to run GenMAPP with the latest C. trachomatis database.
Tab-delimited version of the file above.
Microarray data with identified Gene ID's and Log base data.
version edited during office hours by Dr. Dahlquist to demonstrate statistics
finished version of version edited during office hours by Dr. Dahlquist to demonstrate statistics -- finished by Dillon Williams
Microarray data with separated IDs CTA_#### from _RRMH#####_...
Excel Speadsheet with data formatted for GenMAPP (Version run in GenMAPP).

For GenMAPP Files

EB to RB ATP Metabolic Process Mapp file.
EB to RB glucose catabolic process map.
EB to RB Rifampicin go.txt file.
For_GenMAPP .gex file.
For GenMAPP .gmf file.
Access file created with .gex file.
Color set created in GenMAPP for EB to RB no rifampicin and increased/decreased logFC criteria

MAPPFinder Files

Increased
Deceased
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. 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

[edit] Wiki Formatting

Template: Template:Team_H(oo)KD

Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Chlamydia_trachomatis&oldid=7156"
Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox