LMU BioDB 2015 - User contributions [en]

Template:Heavy Metal HaterZ

2015-12-18T22:25:02Z

Emilysimso: /* Shewanella oneidensis */ formatting

[[Image:HeavyMetal.jpg | 200px | right]]
==''Shewanella oneidensis''==
'''[[Gene Database Testing Report - Heavy Metal HaterZ | Our Gene Database Testing Report ]]'''

'''Group Paper''' - [[File:Final Report 20151218 HMH.docx]]

==Group Members==
*Coder:[[User:Malverso | Mary Alverson]]
*GenMAPP User & Project Manager:[[User:Rlegaspi | Ron Legaspi]]
*Quality Assurance:[[User:Jkuroda | Josh Kuroda]]
*GenMAPP User:[[User:Emilysimso | Emily Simso]]
==Important Links==
====[[Heavy Metal HaterZ Files | Our Files]]====
====[[Heavy Metal HaterZ Deliverables | Our Deliverables]]====
{{Gene_Database_Project_Links}}
{{HMH Individual Journal Entries}}

[[Category:Group Projects]]
[[Category:Heavy Metal HaterZ]]

File:Final Report 20151218 HMH.docx

2015-12-18T22:24:22Z

Emilysimso: Emilysimso uploaded a new version of File:Final Report 20151218 HMH.docx

Template:Heavy Metal HaterZ

2015-12-18T22:22:25Z

Emilysimso: /* Shewanella oneidensis */ formatting

[[Image:HeavyMetal.jpg | 200px | right]]
==''Shewanella oneidensis''==
'''[[Gene Database Testing Report - Heavy Metal HaterZ | Our Gene Database Testing Report ]]'''

'''Group Paper''' - [[File:Final Report 20151218 HMH.docx | Group Paper]]

==Group Members==
*Coder:[[User:Malverso | Mary Alverson]]
*GenMAPP User & Project Manager:[[User:Rlegaspi | Ron Legaspi]]
*Quality Assurance:[[User:Jkuroda | Josh Kuroda]]
*GenMAPP User:[[User:Emilysimso | Emily Simso]]
==Important Links==
====[[Heavy Metal HaterZ Files | Our Files]]====
====[[Heavy Metal HaterZ Deliverables | Our Deliverables]]====
{{Gene_Database_Project_Links}}
{{HMH Individual Journal Entries}}

[[Category:Group Projects]]
[[Category:Heavy Metal HaterZ]]

Template:Heavy Metal HaterZ

2015-12-18T22:20:54Z

Emilysimso: /* Shewanella oneidensis */ added paper link

[[Image:HeavyMetal.jpg | 200px | right]]
==''Shewanella oneidensis''==
'''[[Gene Database Testing Report - Heavy Metal HaterZ | Our Gene Database Testing Report ]]'''

'''[[File:Final Report 20151218 HMH.docx | Group Paper]]'''

==Group Members==
*Coder:[[User:Malverso | Mary Alverson]]
*GenMAPP User & Project Manager:[[User:Rlegaspi | Ron Legaspi]]
*Quality Assurance:[[User:Jkuroda | Josh Kuroda]]
*GenMAPP User:[[User:Emilysimso | Emily Simso]]
==Important Links==
====[[Heavy Metal HaterZ Files | Our Files]]====
====[[Heavy Metal HaterZ Deliverables | Our Deliverables]]====
{{Gene_Database_Project_Links}}
{{HMH Individual Journal Entries}}

[[Category:Group Projects]]
[[Category:Heavy Metal HaterZ]]

File:Final Report 20151218 HMH.docx

2015-12-18T22:18:44Z

Emilysimso:

Heavy Metal HaterZ Deliverables

2015-12-18T22:01:13Z

Emilysimso: /* Individual Assessments and Reflections */ Emily section

{{Template:Heavy Metal HaterZ}}

== Individual Assessments and Reflections ==
[[Malverso Assessments & Reflections]]

[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_15#Statement_of_Work Emily Simso (on Week 15 Assignment Page)]

== Group Files and Datasets ==

===Gene Database===

* [[Media:So-Std_HMH_20151214.zip | GenMAPP Gene Database for assigned species]]
* ReadMe file to accompany the Gene Database (''.pdf'')
** [[Media:ReadMe So-Std 20151214.pdf | Shewanella onedensis ReadMe]]
* [[Media:Gene Database Testing Report - Heavy Metal HaterZ.pdf | Gene Database Testing Report]] for final submitted Gene Database
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
* [[Media:CompiledRawData ForGenMAPP 20151208 HMH.txt | Data file]] used for import into GenMAPP
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.gex | GenMAPP Expression Dataset file]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.EX.txt | Exceptions file]] of data imported into GenMAPP
* Raw MAPPFinder results files:
** [[Media:MAPPFINDER 20151212-Criterion0-GO.txt | criterion 0]]
** [[Media:MAPPFINDER 20151212-Criterion1-GO.txt | criterion 1]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.zip | ''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
**[[Media:MAPPFINDER 20151212-Criterion0-GO.xlsx | criterion 0]]
**[[Media:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx | criterion 1]]
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
**[[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp | Fatty Acid Degradation]]
**[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp | Compiled Fatty Acid Degradation]]
**[[File:Ribosomal Soneidensis 20151213 HMH.mapp | Ribosome]]
**[[File:Compiled Ribosome 20151216 HMH.mapp | Compiled Ribosome]]
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* [[Media:Biol Data Final Presentation.pdf | PowerPoint presentation]] given on Tuesday, December 15

[[Gene Database Project Deliverables]]
[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

Emilysimso Week 15

2015-12-18T21:59:17Z

Emilysimso: /* Statement of Work */ paper comments

==Procedure==
*Calculated averages from split data for each time point and replicate
**Total of 5409 genes
*Calculated biological averages of each time point
*Calculated AverageLogRatio comparing C5, C20, and C60 to C0 and F5, F20, and F60 to C60
**Subtracted not divided due to log space
*Performed TTest on the above relationships to get the Pvalue
*Performed Bonferroni
*Performed Benjamini & Hochberg
*Created new sheet forGenMAPP
**Did adjustments to prepare file for GenMAPP
**Saved as .txt and uploaded to wiki

===GenMAPP===
*Increase criterea = >0.25 AND B-H <0.05
*Decrease criterea <-0.25 AND B-H <0.05
*1441 errors in the raw data
*Red is increased, green is decreased
*Uploaded C5-C0, C20-C0, C60-C0, F5-C60, F20-C60, and F60-C60 into GenMAPP

===MAPPFinder===
*Criteria: Zscore >2, Permute P<0.05, Number Changed > or equal to 4 < or equal to 100, Percent Changed > or equal to 50%

==Files==
*New spreadsheet
**File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx
*Spreadsheet for GenMAPP
**[[File:CompiledRawData WithGenMAPP 20151208 HMH.docx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]

==Individual Reflection==
===Statement of Work===
I was a GenMAPP User for the group project, meaning I did the raw data analysis from the microarray experiment and worked with the program to analyze the results. I compiled the data from the repletion stage of the experiment (all of the F time points - found on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_12 Week 12 page]) and then combined this data with Ron to perform the statistical analysis on the data (found on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_14 Week 14 page]). I also created the file we used for [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:UpdatedCompiledRawData_WithGenMAPP_20151210_ES_HMH.xlsx GenMAPP]. I worked with Josh to enter the data into GenMAPP and then worked with Ron to figure out the criteria for significance of the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion0-GO_20151212_HMH.xlsx increased] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion1-GO_20151212_HMH.xlsx decreased] genes. I also created the MAPPs for the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Fatty_Acid_Degradation_Soneidensis_20151213_HMH.mapp Fatty Acid Degradation] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Ribosomal_Soneidensis_20151213_HMH.mapp Ribosome] gene pathways, as well as the compiled [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Fatty_Acid_Degradation_Compiled_20151216_HMH.PNG Fatty Acid Degradation] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Compiled_Ribosome_Image_20151216_HMH.PNG Ribosome] pathways. Finally, I created the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Experimental_Design_Flow_Chart_20151115_HMH.pptx experimental design flow chart].

I also wrote the vast majority of the paper, compiled all of the tables and figures, and led the group for this portion.

===Assessment of Project===
I think our group worked fairly well together, but we had some issues with communication. Everyone was responsible and got their work done, but sometimes it was unclear when things would be finished or who needed to do which task. There were also some problems with direction and we could have used someone taking a stronger leadership role. I think we should have met more together outside of class to clear up some of these issues, so I would have definitely done that differently. Specifically, Ron and I should have met more to work on the Excel files, since it was unnecessarily complicated doing it apart from each other. Overall, however, I think our group was able to work together to finish the project.

Our Gene Database Project was mostly complete, however, we were missing the compiled MAPPFinder files for the Ribosome and Fatty Acid Degradation pathways. We also could have done a more thorough comparison between our results and the Yang et al. microarray data. I think our overall quality was fairly high and our organization worked well. Our Group Paper was more complete than the presentation because we added the elements initially missing. I think we could have gone further in our analysis, but the rest of the group thought that might be unnecessary.

===Reflection on the Process===
I learned a lot from this project and I think the class as a whole will stay with me beyond undergrad. This course helped solidify the connection between biology and computer science, which is something I had not previously thought much about. I think I learned more about computer science overall, as I had not been exposed to that field before, in terms of database construction, coding, and how various programs can be put together for a final result. In terms of teamwork, this project reminded me how important it is to use people’s skills and work together to make the best project. This project was very specialized, so building off of individual knowledge definitely helped. I think this will help with future projects, especially as they become more involved and specific. I was also reminded about my own leadership style and group role. For technical skills, I learned how to do some basic coding, database construction, and analysis of a species’ genome. Learning to interpret genomic data is an important skill to start building, as the field is always growing and becoming increasingly relevant to biology.

The biggest lesson I will take away is that even if a project seems daunting, it can be tackled; before coming into this course, I knew very little about computer science and databases, so having a finished product is very rewarding.

{{Template: Esimso entries etc}}

Heavy Metal HaterZ Deliverables

2015-12-18T21:23:02Z

Emilysimso: /* Group Files and Datasets */ formatting

{{Template:Heavy Metal HaterZ}}

== Individual Assessments and Reflections ==
[[Malverso Assessments & Reflections]]

== Group Files and Datasets ==

===Gene Database===

* [[Media:So-Std_HMH_20151214.zip | GenMAPP Gene Database for assigned species]]
* ReadMe file to accompany the Gene Database (''.pdf'')
** [[Media:ReadMe So-Std 20151214.pdf | Shewanella onedensis ReadMe]]
* [[Media:Gene Database Testing Report - Heavy Metal HaterZ.pdf | Gene Database Testing Report]] for final submitted Gene Database
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
* [[Media:CompiledRawData ForGenMAPP 20151208 HMH.txt | Data file]] used for import into GenMAPP
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.gex | GenMAPP Expression Dataset file]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.EX.txt | Exceptions file]] of data imported into GenMAPP
* Raw MAPPFinder results files:
** [[Media:MAPPFINDER 20151212-Criterion0-GO.txt | criterion 0]]
** [[Media:MAPPFINDER 20151212-Criterion1-GO.txt | criterion 1]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.zip | ''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
**[[Media:MAPPFINDER 20151212-Criterion0-GO.xlsx | criterion 0]]
**[[Media:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx | criterion 1]]
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
**[[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp | Fatty Acid Degradation]]
**[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp | Compiled Fatty Acid Degradation]]
**[[File:Ribosomal Soneidensis 20151213 HMH.mapp | Ribosome]]
**[[File:Compiled Ribosome 20151216 HMH.mapp | Compiled Ribosome]]
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* [[Media:Biol Data Final Presentation.pdf | PowerPoint presentation]] given on Tuesday, December 15

[[Gene Database Project Deliverables]]
[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

Heavy Metal HaterZ Deliverables

2015-12-18T21:22:32Z

Emilysimso: /* Group Files and Datasets */ added file

{{Template:Heavy Metal HaterZ}}

== Individual Assessments and Reflections ==
[[Malverso Assessments & Reflections]]

== Group Files and Datasets ==

===Gene Database===

* [[Media:So-Std_HMH_20151214.zip | GenMAPP Gene Database for assigned species]]
* ReadMe file to accompany the Gene Database (''.pdf'')
** [[Media:ReadMe So-Std 20151214.pdf | Shewanella onedensis ReadMe]]
* [[Media:Gene Database Testing Report - Heavy Metal HaterZ.pdf | Gene Database Testing Report]] for final submitted Gene Database
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
**File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx
* [[Media:CompiledRawData ForGenMAPP 20151208 HMH.txt | Data file]] used for import into GenMAPP
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.gex | GenMAPP Expression Dataset file]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.EX.txt | Exceptions file]] of data imported into GenMAPP
* Raw MAPPFinder results files:
** [[Media:MAPPFINDER 20151212-Criterion0-GO.txt | criterion 0]]
** [[Media:MAPPFINDER 20151212-Criterion1-GO.txt | criterion 1]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.zip | ''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
**[[Media:MAPPFINDER 20151212-Criterion0-GO.xlsx | criterion 0]]
**[[Media:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx | criterion 1]]
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
**[[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp | Fatty Acid Degradation]]
**[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp | Compiled Fatty Acid Degradation]]
**[[File:Ribosomal Soneidensis 20151213 HMH.mapp | Ribosome]]
**[[File:Compiled Ribosome 20151216 HMH.mapp | Compiled Ribosome]]
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* [[Media:Biol Data Final Presentation.pdf | PowerPoint presentation]] given on Tuesday, December 15

[[Gene Database Project Deliverables]]
[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

File:Experimental Design Flow Chart 20151115 HMH.pptx

2015-12-18T18:40:46Z

Emilysimso: Emilysimso uploaded a new version of File:Experimental Design Flow Chart 20151115 HMH.pptx

Heavy Metal HaterZ Deliverables

2015-12-18T18:04:57Z

Emilysimso: /* Gene Database */ formatting

{{Template:Heavy Metal HaterZ}}

== Individual Assessments and Reflections ==
[[Malverso Assessments & Reflections]]

== Group Files and Datasets ==

===Gene Database===

* [[Media:So-Std_HMH_20151214.zip | GenMAPP Gene Database for assigned species]]
* ReadMe file to accompany the Gene Database (''.pdf'')
** [[Media:ReadMe So-Std 20151214.pdf | Shewanella onedensis ReadMe]]
* [[Media:Gene Database Testing Report - Heavy Metal HaterZ.pdf | Gene Database Testing Report]] for final submitted Gene Database
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* [[Media:CompiledRawData ForGenMAPP 20151208 HMH.txt | Data file]] used for import into GenMAPP
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.gex | GenMAPP Expression Dataset file]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.EX.txt | Exceptions file]] of data imported into GenMAPP
* Raw MAPPFinder results files:
** [[Media:MAPPFINDER 20151212-Criterion0-GO.txt | criterion 0]]
** [[Media:MAPPFINDER 20151212-Criterion1-GO.txt | criterion 1]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.zip | ''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
**[[Media:MAPPFINDER 20151212-Criterion0-GO.xlsx | criterion 0]]
**[[Media:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx | criterion 1]]
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
**[[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp | Fatty Acid Degradation]]
**[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp | Compiled Fatty Acid Degradation]]
**[[File:Ribosomal Soneidensis 20151213 HMH.mapp | Ribosome]]
**[[File:Compiled Ribosome 20151216 HMH.mapp | Compiled Ribosome]]
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* [[Media:Biol Data Final Presentation.pdf | PowerPoint presentation]] given on Tuesday, December 15

[[Gene Database Project Deliverables]]
[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

Heavy Metal HaterZ Deliverables

2015-12-18T18:02:13Z

Emilysimso: /* Group Files and Datasets */ formatting

{{Template:Heavy Metal HaterZ}}

== Individual Assessments and Reflections ==
[[Malverso Assessments & Reflections]]

== Group Files and Datasets ==

===Gene Database===

* [[Media:So-Std_HMH_20151214.zip | GenMAPP Gene Database for assigned species]]
* ReadMe file to accompany the Gene Database (''.pdf'')
** [[Media:ReadMe So-Std 20151214.pdf | Shewanella onedensis ReadMe]]
* [[Media:Gene Database Testing Report - Heavy Metal HaterZ.pdf | Gene Database Testing Report]] for final submitted Gene Database
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* [[Media:CompiledRawData ForGenMAPP 20151208 HMH.txt | Data file]] used for import into GenMAPP
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.gex | GenMAPP Expression Dataset file]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.EX.txt | Exceptions file]] of data imported into GenMAPP
* Raw MAPPFinder results files:
** [[Media:MAPPFINDER 20151212-Criterion0-GO.txt | criterion 0]]
** [[Media:MAPPFINDER 20151212-Criterion1-GO.txt | criterion 1]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.zip | ''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
**[[Media:MAPPFINDER 20151212-Criterion0-GO.xlsx | criterion 0]]
**[[Media:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx | criterion 1]]
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
**[[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp Fatty Acid Degradation]]
**[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp Compiled Fatty Acid Degradation]]
**[[File:Ribosomal Soneidensis 20151213 HMH.mapp Ribosome]]
**[[File:Compiled Ribosome 20151216 HMH.mapp Compiled Ribosome]]
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* [[Media:Biol Data Final Presentation.pdf | PowerPoint presentation]] given on Tuesday, December 15

[[Gene Database Project Deliverables]]
[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

Heavy Metal HaterZ Deliverables

2015-12-18T18:01:39Z

Emilysimso: /* Group Files and Datasets */ added mapps

{{Template:Heavy Metal HaterZ}}

== Individual Assessments and Reflections ==
[[Malverso Assessments & Reflections]]

== Group Files and Datasets ==

===Gene Database===

* [[Media:So-Std_HMH_20151214.zip | GenMAPP Gene Database for assigned species]]
* ReadMe file to accompany the Gene Database (''.pdf'')
** [[Media:ReadMe So-Std 20151214.pdf | Shewanella onedensis ReadMe]]
* [[Media:Gene Database Testing Report - Heavy Metal HaterZ.pdf | Gene Database Testing Report]] for final submitted Gene Database
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* [[Media:CompiledRawData ForGenMAPP 20151208 HMH.txt | Data file]] used for import into GenMAPP
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.gex | GenMAPP Expression Dataset file]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.EX.txt | Exceptions file]] of data imported into GenMAPP
* Raw MAPPFinder results files:
** [[Media:MAPPFINDER 20151212-Criterion0-GO.txt | criterion 0]]
** [[Media:MAPPFINDER 20151212-Criterion1-GO.txt | criterion 1]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.zip | ''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
**[[Media:MAPPFINDER 20151212-Criterion0-GO.xlsx | criterion 0]]
**[[Media:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx | criterion 1]]
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
**[[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp | Fatty Acid Degradation]]
**[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp | Compiled Fatty Acid Degradation]]
**[[File:Ribosomal Soneidensis 20151213 HMH.mapp | Ribosome]]
**[[File:Compiled Ribosome 20151216 HMH.mapp | Compiled Ribosome]]
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* [[Media:Biol Data Final Presentation.pdf | PowerPoint presentation]] given on Tuesday, December 15

[[Gene Database Project Deliverables]]
[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

Emilysimso Week 15

2015-12-18T08:10:24Z

Emilysimso: /* Individual Reflection */ finished reflection

==Procedure==
*Calculated averages from split data for each time point and replicate
**Total of 5409 genes
*Calculated biological averages of each time point
*Calculated AverageLogRatio comparing C5, C20, and C60 to C0 and F5, F20, and F60 to C60
**Subtracted not divided due to log space
*Performed TTest on the above relationships to get the Pvalue
*Performed Bonferroni
*Performed Benjamini & Hochberg
*Created new sheet forGenMAPP
**Did adjustments to prepare file for GenMAPP
**Saved as .txt and uploaded to wiki

===GenMAPP===
*Increase criterea = >0.25 AND B-H <0.05
*Decrease criterea <-0.25 AND B-H <0.05
*1441 errors in the raw data
*Red is increased, green is decreased
*Uploaded C5-C0, C20-C0, C60-C0, F5-C60, F20-C60, and F60-C60 into GenMAPP

===MAPPFinder===
*Criteria: Zscore >2, Permute P<0.05, Number Changed > or equal to 4 < or equal to 100, Percent Changed > or equal to 50%

==Files==
*New spreadsheet
**File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx
*Spreadsheet for GenMAPP
**[[File:CompiledRawData WithGenMAPP 20151208 HMH.docx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]

==Individual Reflection==
===Statement of Work===
I was a GenMAPP User for the group project, meaning I did the raw data analysis from the microarray experiment and worked with the program to analyze the results. I compiled the data from the repletion stage of the experiment (all of the F time points - found on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_12 Week 12 page]) and then combined this data with Ron to perform the statistical analysis on the data (found on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_14 Week 14 page]). I also created the file we used for [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:UpdatedCompiledRawData_WithGenMAPP_20151210_ES_HMH.xlsx GenMAPP]. I worked with Josh to enter the data into GenMAPP and then worked with Ron to figure out the criteria for significance of the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion0-GO_20151212_HMH.xlsx increased] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion1-GO_20151212_HMH.xlsx decreased] genes. I also created the MAPPs for the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Fatty_Acid_Degradation_Soneidensis_20151213_HMH.mapp Fatty Acid Degradation] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Ribosomal_Soneidensis_20151213_HMH.mapp Ribosome] gene pathways, as well as the compiled [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Fatty_Acid_Degradation_Compiled_20151216_HMH.PNG Fatty Acid Degradation] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Compiled_Ribosome_Image_20151216_HMH.PNG Ribosome] pathways. Finally, I created the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Experimental_Design_Flow_Chart_20151115_HMH.pptx experimental design flow chart].

===Assessment of Project===
I think our group worked fairly well together, but we had some issues with communication. Everyone was responsible and got their work done, but sometimes it was unclear when things would be finished or who needed to do which task. There were also some problems with direction and we could have used someone taking a stronger leadership role. I think we should have met more together outside of class to clear up some of these issues, so I would have definitely done that differently. Specifically, Ron and I should have met more to work on the Excel files, since it was unnecessarily complicated doing it apart from each other. Overall, however, I think our group was able to work together to finish the project.

Our Gene Database Project was mostly complete, however, we were missing the compiled MAPPFinder files for the Ribosome and Fatty Acid Degradation pathways. We also could have done a more thorough comparison between our results and the Yang et al. microarray data. I think our overall quality was fairly high and our organization worked well. Our Group Paper was more complete than the presentation because we added the elements initially missing. I think we could have gone further in our analysis, but the rest of the group thought that might be unnecessary.

===Reflection on the Process===
I learned a lot from this project and I think the class as a whole will stay with me beyond undergrad. This course helped solidify the connection between biology and computer science, which is something I had not previously thought much about. I think I learned more about computer science overall, as I had not been exposed to that field before, in terms of database construction, coding, and how various programs can be put together for a final result. In terms of teamwork, this project reminded me how important it is to use people’s skills and work together to make the best project. This project was very specialized, so building off of individual knowledge definitely helped. I think this will help with future projects, especially as they become more involved and specific. I was also reminded about my own leadership style and group role. For technical skills, I learned how to do some basic coding, database construction, and analysis of a species’ genome. Learning to interpret genomic data is an important skill to start building, as the field is always growing and becoming increasingly relevant to biology.

The biggest lesson I will take away is that even if a project seems daunting, it can be tackled; before coming into this course, I knew very little about computer science and databases, so having a finished product is very rewarding.

{{Template: Esimso entries etc}}

Heavy Metal HaterZ Files

2015-12-16T23:04:35Z

Emilysimso: /* Tables for Paper */ added ribosome table

==All Files==
*All files will be listed here.
*Appropriate way to title files:
**FileName_YYYYMMDD_HMH

===Gene Database===
*[[File:So-Std_HMH_20151214.zip]]

===Initial Flow Chart===
*Initial flow chart for experimental design - [[File:Experimental Design Flow Chart 20151115 HMH.pptx]]

===Journal Club Presentation Power Points===
*Microarray Paper Presentation - [[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]
*Genome Paper Presentation - [[File:GenomePPT_20151123_HMH.pdf]]

===Data Processing Notes from Dr. Dahlquist===
*Page 1 of Notes - [[Media:DrDDataProcessNotes1 20151119 HMH.JPG]]
*Page 2 of Notes - [[Media:DrDDataProcessNotes2 20151119 HMH.JPG]]

===GenMapp Builder===
*[[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]

===Statistical Analysis Excel Sheets===
*Prior to Splitting:
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData 20151206 HMH.xlsx]]
* After splitting, use this one:
*# [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx]]
*Following the splitting, averages taken and ttests done to data sets:
*#[[File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx]]
*#* [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx]]
*#* I made corrections to Emily's file because there are 5408 genes, not 5408. I think that both files have the same results not and you can move on to the next step. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:22, 9 December 2015 (PST)''
*Ready for GenMAPP
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]
* Ranked List from MAPPFinder: [[File:Ranked list from MAPPFinder.PNG]]

===Sanity Check Table===
*[[File:Sanity Check Chart 20151212 HMH.xlsx]]

===MAPPFinder Documents===
*gdb file - [[File:So-Std 20151201special.zip]]
*[[File:ColorSetforExpressionData F60C60 20151210 HMH.gex]]
*GenMAPP with all comparisons - [[File:FilesForComparison AllTrials WithGenMAPP 20151212 ES HMH.gex]]
*Filtered GO terms for increased - [[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.txt]]
*Filtered GO terms for decreased - [[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt]]
*Screenshots showing significant results - [[File:CompiledScreenShots 20151212 HMH.docx]]
*MAPP for Fatty Acid Degradation - [[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation 20151214 HMH.PNG]]
*MAPP for Ribosome - [[File:Ribosomal Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Ribosomal Pathway 20151213 HMH.PNG]]
*MAPP for Compiled Ribosome - [[File:Compiled Ribosome 20151216 HMH.mapp]]
**Screenshot of results - [[File:Compiled Ribosome Image 20151216 HMH.PNG]]
*MAPP for Compiled Fatty Acid Degradation -[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation Compiled 20151216 HMH.PNG]]

===KEGG Screenshots===
*Fatty Acid Degradation [[File:Fatty Acid Pathway from KEGG 20151216 HMH.PNG]]
*Ribosome [[File:Ribosome Pathway from KEGG 20151216 HMH.PNG]]

===Tables for Paper===
*Table showing variations between Yang et al. paper for 6 chosen genes and our results - [[File:Gene Comparison 20151216 HMH.xlsx]]
*Tale showing variations between Yang et al. paper for genes involved in the ribosome pathway and our results - [[File:Ribosome Pathway Comparison 20151216 HMH.xlsx]]

[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

File:Ribosome Pathway Comparison 20151216 HMH.xlsx

2015-12-16T23:03:37Z

Emilysimso:

Heavy Metal HaterZ Files

2015-12-16T22:49:11Z

Emilysimso: added section/file

==All Files==
*All files will be listed here.
*Appropriate way to title files:
**FileName_YYYYMMDD_HMH

===Gene Database===
*[[File:So-Std_HMH_20151214.zip]]

===Initial Flow Chart===
*Initial flow chart for experimental design - [[File:Experimental Design Flow Chart 20151115 HMH.pptx]]

===Journal Club Presentation Power Points===
*Microarray Paper Presentation - [[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]
*Genome Paper Presentation - [[File:GenomePPT_20151123_HMH.pdf]]

===Data Processing Notes from Dr. Dahlquist===
*Page 1 of Notes - [[Media:DrDDataProcessNotes1 20151119 HMH.JPG]]
*Page 2 of Notes - [[Media:DrDDataProcessNotes2 20151119 HMH.JPG]]

===GenMapp Builder===
*[[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]

===Statistical Analysis Excel Sheets===
*Prior to Splitting:
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData 20151206 HMH.xlsx]]
* After splitting, use this one:
*# [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx]]
*Following the splitting, averages taken and ttests done to data sets:
*#[[File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx]]
*#* [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx]]
*#* I made corrections to Emily's file because there are 5408 genes, not 5408. I think that both files have the same results not and you can move on to the next step. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:22, 9 December 2015 (PST)''
*Ready for GenMAPP
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]
* Ranked List from MAPPFinder: [[File:Ranked list from MAPPFinder.PNG]]

===Sanity Check Table===
*[[File:Sanity Check Chart 20151212 HMH.xlsx]]

===MAPPFinder Documents===
*gdb file - [[File:So-Std 20151201special.zip]]
*[[File:ColorSetforExpressionData F60C60 20151210 HMH.gex]]
*GenMAPP with all comparisons - [[File:FilesForComparison AllTrials WithGenMAPP 20151212 ES HMH.gex]]
*Filtered GO terms for increased - [[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.txt]]
*Filtered GO terms for decreased - [[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt]]
*Screenshots showing significant results - [[File:CompiledScreenShots 20151212 HMH.docx]]
*MAPP for Fatty Acid Degradation - [[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation 20151214 HMH.PNG]]
*MAPP for Ribosome - [[File:Ribosomal Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Ribosomal Pathway 20151213 HMH.PNG]]
*MAPP for Compiled Ribosome - [[File:Compiled Ribosome 20151216 HMH.mapp]]
**Screenshot of results - [[File:Compiled Ribosome Image 20151216 HMH.PNG]]
*MAPP for Compiled Fatty Acid Degradation -[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation Compiled 20151216 HMH.PNG]]

===KEGG Screenshots===
*Fatty Acid Degradation [[File:Fatty Acid Pathway from KEGG 20151216 HMH.PNG]]
*Ribosome [[File:Ribosome Pathway from KEGG 20151216 HMH.PNG]]

===Tables for Paper===
*Table showing variations between Yang et al. paper for 6 chosen genes and our results - [[File:Gene Comparison 20151216 HMH.xlsx]]

[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

File:Gene Comparison 20151216 HMH.xlsx

2015-12-16T22:48:06Z

Emilysimso:

Heavy Metal HaterZ Files

2015-12-16T21:42:03Z

Emilysimso: added KEGG screenshots

==All Files==
*All files will be listed here.
*Appropriate way to title files:
**FileName_YYYYMMDD_HMH

===Gene Database===
*[[File:So-Std_HMH_20151214.zip]]

===Initial Flow Chart===
*Initial flow chart for experimental design - [[File:Experimental Design Flow Chart 20151115 HMH.pptx]]

===Journal Club Presentation Power Points===
*Microarray Paper Presentation - [[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]
*Genome Paper Presentation - [[File:GenomePPT_20151123_HMH.pdf]]

===Data Processing Notes from Dr. Dahlquist===
*Page 1 of Notes - [[Media:DrDDataProcessNotes1 20151119 HMH.JPG]]
*Page 2 of Notes - [[Media:DrDDataProcessNotes2 20151119 HMH.JPG]]

===GenMapp Builder===
*[[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]

===Statistical Analysis Excel Sheets===
*Prior to Splitting:
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData 20151206 HMH.xlsx]]
* After splitting, use this one:
*# [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx]]
*Following the splitting, averages taken and ttests done to data sets:
*#[[File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx]]
*#* [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx]]
*#* I made corrections to Emily's file because there are 5408 genes, not 5408. I think that both files have the same results not and you can move on to the next step. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:22, 9 December 2015 (PST)''
*Ready for GenMAPP
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]
* Ranked List from MAPPFinder: [[File:Ranked list from MAPPFinder.PNG]]

===Sanity Check Table===
*[[File:Sanity Check Chart 20151212 HMH.xlsx]]

===MAPPFinder Documents===
*gdb file - [[File:So-Std 20151201special.zip]]
*[[File:ColorSetforExpressionData F60C60 20151210 HMH.gex]]
*GenMAPP with all comparisons - [[File:FilesForComparison AllTrials WithGenMAPP 20151212 ES HMH.gex]]
*Filtered GO terms for increased - [[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.txt]]
*Filtered GO terms for decreased - [[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt]]
*Screenshots showing significant results - [[File:CompiledScreenShots 20151212 HMH.docx]]
*MAPP for Fatty Acid Degradation - [[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation 20151214 HMH.PNG]]
*MAPP for Ribosome - [[File:Ribosomal Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Ribosomal Pathway 20151213 HMH.PNG]]
*MAPP for Compiled Ribosome - [[File:Compiled Ribosome 20151216 HMH.mapp]]
**Screenshot of results - [[File:Compiled Ribosome Image 20151216 HMH.PNG]]
*MAPP for Compiled Fatty Acid Degradation -[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation Compiled 20151216 HMH.PNG]]

===KEGG Screenshots===
*Fatty Acid Degradation [[File:Fatty Acid Pathway from KEGG 20151216 HMH.PNG]]
*Ribosome [[File:Ribosome Pathway from KEGG 20151216 HMH.PNG]]

[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

File:Ribosome Pathway from KEGG 20151216 HMH.PNG

2015-12-16T21:41:48Z

Emilysimso:

File:Fatty Acid Pathway from KEGG 20151216 HMH.PNG

2015-12-16T21:41:01Z

Emilysimso:

Heavy Metal HaterZ Files

2015-12-16T21:39:21Z

Emilysimso: /* MAPPFinder Documents */ added compiled fatty acid degradation

==All Files==
*All files will be listed here.
*Appropriate way to title files:
**FileName_YYYYMMDD_HMH

===Gene Database===
*[[File:So-Std_HMH_20151214.zip]]

===Initial Flow Chart===
*Initial flow chart for experimental design - [[File:Experimental Design Flow Chart 20151115 HMH.pptx]]

===Journal Club Presentation Power Points===
*Microarray Paper Presentation - [[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]
*Genome Paper Presentation - [[File:GenomePPT_20151123_HMH.pdf]]

===Data Processing Notes from Dr. Dahlquist===
*Page 1 of Notes - [[Media:DrDDataProcessNotes1 20151119 HMH.JPG]]
*Page 2 of Notes - [[Media:DrDDataProcessNotes2 20151119 HMH.JPG]]

===GenMapp Builder===
*[[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]

===Statistical Analysis Excel Sheets===
*Prior to Splitting:
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData 20151206 HMH.xlsx]]
* After splitting, use this one:
*# [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx]]
*Following the splitting, averages taken and ttests done to data sets:
*#[[File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx]]
*#* [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx]]
*#* I made corrections to Emily's file because there are 5408 genes, not 5408. I think that both files have the same results not and you can move on to the next step. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:22, 9 December 2015 (PST)''
*Ready for GenMAPP
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]
* Ranked List from MAPPFinder: [[File:Ranked list from MAPPFinder.PNG]]

===Sanity Check Table===
*[[File:Sanity Check Chart 20151212 HMH.xlsx]]

===MAPPFinder Documents===
*gdb file - [[File:So-Std 20151201special.zip]]
*[[File:ColorSetforExpressionData F60C60 20151210 HMH.gex]]
*GenMAPP with all comparisons - [[File:FilesForComparison AllTrials WithGenMAPP 20151212 ES HMH.gex]]
*Filtered GO terms for increased - [[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.txt]]
*Filtered GO terms for decreased - [[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt]]
*Screenshots showing significant results - [[File:CompiledScreenShots 20151212 HMH.docx]]
*MAPP for Fatty Acid Degradation - [[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation 20151214 HMH.PNG]]
*MAPP for Ribosome - [[File:Ribosomal Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Ribosomal Pathway 20151213 HMH.PNG]]
*MAPP for Compiled Ribosome - [[File:Compiled Ribosome 20151216 HMH.mapp]]
**Screenshot of results - [[File:Compiled Ribosome Image 20151216 HMH.PNG]]
*MAPP for Compiled Fatty Acid Degradation -[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation Compiled 20151216 HMH.PNG]]

[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

File:Fatty Acid Degradation Compiled 20151216 HMH.PNG

2015-12-16T21:39:06Z

Emilysimso:

File:Compiled Fatty Acid Degradation 20151216 HMH.mapp

2015-12-16T21:38:26Z

Emilysimso:

Heavy Metal HaterZ Files

2015-12-16T21:36:30Z

Emilysimso: /* MAPPFinder Documents */ added compiled ribosome

==All Files==
*All files will be listed here.
*Appropriate way to title files:
**FileName_YYYYMMDD_HMH

===Gene Database===
*[[File:So-Std_HMH_20151214.zip]]

===Initial Flow Chart===
*Initial flow chart for experimental design - [[File:Experimental Design Flow Chart 20151115 HMH.pptx]]

===Journal Club Presentation Power Points===
*Microarray Paper Presentation - [[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]
*Genome Paper Presentation - [[File:GenomePPT_20151123_HMH.pdf]]

===Data Processing Notes from Dr. Dahlquist===
*Page 1 of Notes - [[Media:DrDDataProcessNotes1 20151119 HMH.JPG]]
*Page 2 of Notes - [[Media:DrDDataProcessNotes2 20151119 HMH.JPG]]

===GenMapp Builder===
*[[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]

===Statistical Analysis Excel Sheets===
*Prior to Splitting:
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData 20151206 HMH.xlsx]]
* After splitting, use this one:
*# [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx]]
*Following the splitting, averages taken and ttests done to data sets:
*#[[File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx]]
*#* [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx]]
*#* I made corrections to Emily's file because there are 5408 genes, not 5408. I think that both files have the same results not and you can move on to the next step. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:22, 9 December 2015 (PST)''
*Ready for GenMAPP
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]
* Ranked List from MAPPFinder: [[File:Ranked list from MAPPFinder.PNG]]

===Sanity Check Table===
*[[File:Sanity Check Chart 20151212 HMH.xlsx]]

===MAPPFinder Documents===
*gdb file - [[File:So-Std 20151201special.zip]]
*[[File:ColorSetforExpressionData F60C60 20151210 HMH.gex]]
*GenMAPP with all comparisons - [[File:FilesForComparison AllTrials WithGenMAPP 20151212 ES HMH.gex]]
*Filtered GO terms for increased - [[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.txt]]
*Filtered GO terms for decreased - [[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt]]
*Screenshots showing significant results - [[File:CompiledScreenShots 20151212 HMH.docx]]
*MAPP for Fatty Acid Degradation - [[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation 20151214 HMH.PNG]]
*MAPP for Ribosome - [[File:Ribosomal Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Ribosomal Pathway 20151213 HMH.PNG]]
*MAPP for Compiled Ribosome - [[File:Compiled Ribosome 20151216 HMH.mapp]]
**Screenshot of results - [[File:Compiled Ribosome Image 20151216 HMH.PNG]]

[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

File:Compiled Ribosome 20151216 HMH.mapp

2015-12-16T21:36:17Z

Emilysimso:

File:Compiled Ribosome Image 20151216 HMH.PNG

2015-12-16T21:35:17Z

Emilysimso:

File:Ribosomal Pathway 20151213 HMH.PNG

2015-12-16T18:00:00Z

Emilysimso: Emilysimso uploaded a new version of File:Ribosomal Pathway 20151213 HMH.PNG

File:Fatty Acid Degradation 20151214 HMH.PNG

2015-12-16T17:59:30Z

Emilysimso: Emilysimso uploaded a new version of File:Fatty Acid Degradation 20151214 HMH.PNG

File:Ribosomal Soneidensis 20151213 HMH.mapp

2015-12-16T17:57:40Z

Emilysimso: Emilysimso uploaded a new version of File:Ribosomal Soneidensis 20151213 HMH.mapp

File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp

2015-12-16T17:57:20Z

Emilysimso: Emilysimso uploaded a new version of File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp

Heavy Metal HaterZ

2015-12-15T05:49:26Z

Emilysimso: /* Status Report */ added Emily and Ron

{{Heavy Metal HaterZ}}
==Week 15 Assignment==
===Goals===
*Finish Deliverables
*Prepare for the presentation
===Status Report===
*Mary - Finished second customization for the S.oneidensis profile. I need to push it to github with support from Dr.Dionisio.
*Josh - Uploaded most of our deliverables and completed any of the remaining tasks, e.g. ReadMe to accompany the Gene Database
*Emily - Worked on GenMAPP, creating gene pathways, presentation
*Ron - Worked on sanity check, presentation, MAPPFinder

==Week 14 Assignment==
===Goals===
*Coder/QA
**Analyze the initial exports and make any necessary changes to the custom species profile to capture all of the IDs for your species
*GenMAPP Users
**Finish statistical analysis of compiled microarray data
**Prepare file for GenMAPP
===Status Report===
*Mary- I finished customizing the genMappBuilder and uploaded it onto this wiki so htat Josh could test to see if it works, which it does for the most part. A few genes aren't picked up that are not in the MOD but present elsewhere.
* Josh- Completed the export using the customized GenMAPP Builder from Mary. Checked the .gdb file and everything checked out. Used GenMAPP to see if the gene ID links worked and they did. Made more progress on the Gene Database Testing Report.
*Emily - I worked on manipulating the data to import it into GenMAPP and while Ron and I initially had some problems, I think we worked them out and are ready to continue this coming week.
*Ron - Worked on manipulation of the data along with Emily to prepare data for GenMAPP. Difficulties arose when it came to performing particular calculations and having data match with Emily's, but I think that they have been resolved with the help of Dr. Dahlquist; thus, we are closer to having a GenMAPP ready file.

====Reflections====
#What worked?
#What didn't work?
#What will I do next to fix what didn't work?

*Mary:
*#Dr.Dionisio's instructions were very clear so I was able to customize the genMappBuilder and it is working like it should.
*#There are still 11 "lost" genes that may need to be "found" somehow with my code, even though they are not located within the MOD.
*#First I need to determine if those genes are necessary for genMapp to catch, and then i will need to re-customize the code if so.

*Josh:
*# Our customized export seemed to work, since we got the 4196 count for Ordered Locus Names for which we were looking.
*#The 11 IDs we found that did not have gene tags in the XML file are a small issue for us. None of them exist in our model organism database, but 8 of them are present in our microarray data.
*#We are waiting on input from Professor Dahlquist regarding our next steps with these 11 IDs. Once we find out, we will act accordingly and possibly edit our code.

*Emily
*#It was very helpful to have Dr. Dahlquist's instructions for manipulating our data, so I was able to calculate the Pvalues and adjust them using the two tests.
*#Ron and I had to do a lot of work late this week to make our data match, but we worked together well and were able to solve the problems we encountered.
*#I will redo the Pvalues and the two adjustment calculations. Then I will get the data ready for GenMAPP.

*Ron
*#Dr. Dahlquist's instructions and feedback helped with ensuring the manipulation of the data was done accurately.
*#It was difficult to calculate the averages from the split data since the equations wouldn't copy down the entire column due to blank spaces within the data; in addition, calculating the p-values was difficult. In addition, there was a lot of work to be done since issues were encountered with the data and the equations.
*#Hopefully, after all the feedback and instructions Emily and I will be able to do all the necessary calculations and statistical analysis to have a file ready for GenMAPP by the end of this week.

==Week 12 Assignment==
===Goals===
*Coder/QA
**Prepare for journal club presentation
**Perform an initial Gene Database export and Gene Database Testing Report
*GenMAPP Users
**Compile the raw data in preparation for normalization and statistical analysis.
===Status Report===
*Emily: uploaded and formatted all microarray files after they were repleted with ferrous sulfate
*Mary: Prepared for genome paper journal club presentation. I also pushed the code from github onto a computer in the lab, which included downloading eclipse and git for windows on the lab computer.
*Josh: Prepared for genome paper presentation with Mary. Completed the initial import/export cycle and made significant progress on the Gene Database Testing Report.
*Ron: Similar to Emily, downloaded the microarray raw data files, followed the procedure given by Dr. Dahlquist for data processing (I worked with the files related to iron depletion with the iron chelator), and I uploaded the files to the wiki.

==Week 11 Assignment : Journal Club Presentation==
===Presentation Slides===
*These can also be accessed by going to our [[Heavy Metal HaterZ Files | Files]] page.

*[[File:Genome_Paper_Presentation_20151124_HMH.pptx]]
*[[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]

===Goals===
*Prepare for journal club presentations
*Begin initial tasks on your research project
**Coder/QA
***Set up coding/testing environment
***Determine the regular expression for the ordered locus ID for your species
***Identify the appropriate model organism database for your species.
***Perform an initial Gene Database export and Gene Database Testing Report
**GenMAPP Users
***Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
***Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
***Compile the raw data in preparation for normalization and statistical analysis.
===Status Report===
*Emily: worked on journal club presentation and created flow chart diagrams for the experimental design
*Mary: Completed journal club presentation slides with Josh. I downloaded eclipse on my personal laptop, so along with the use of the lab computers my coding/testing environment should be set up. I determined with Josh the regular expression of the ordered locus ID for our species. I was not able to, however, perform an initial export yet.
*Ron: Completed journal club presentation slides with Emily and uploaded slides in HMH Files pages. [[Media:SoMicroarrayPaperPresentation 20151117 HMH.pptx | Link to Microarray Paper Presentation here.]] Looked over sample and data relationships file from ArrayExpress entry (E-GEOD-15334) and converted .txt file into .xlsx file. I have not been able to compile raw data with Emily, as we still need clarification on which files are to be used for statistical analysis.
*Josh: Completed the genome paper presentation with Mary and did more research on our organism. Haven't done an initial import/export cycle yet. Planning to complete that later this week.

==Week 10 Assignment : Annotated Bibliography==

===Our Genome Paper===

Heidelberg, J. F., Paulsen, I. T., Nelson, K. E., Gaidos, E. J., Nelson, W. C., Read, T. D., ... & Fraser, C. M. (2002). Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. ''Nature biotechnology, 20''(11), 1118-1123. doi:10.1038/nbt749
*The [http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+the+dissimilatory+metal+ion%E2%80%93reducing+bacterium+Shewanella+oneidensis abstract] from PubMed.
*The full text of the article in PubMedCentral : Not available.
*The [http://www.nature.com/nbt/journal/v20/n11/full/nbt749.html full text] of the article from the publisher web site. 
*The [http://www.nature.com/nbt/journal/v20/n11/pdf/nbt749.pdf full PDF version] of the article from the publisher web site.
*Who owns the rights to the article?
**The Nature Publishing Group, which is the publisher of this article, according to this [https://s100.copyright.com/AppDispatchServlet?publisherName=NPG&publication=Nature%20Biotechnology&title=Genome%20sequence%20of%20the%20dissimilatory%20metal%20ion-reducing%20bacterium%20Shewanella%20oneidensis&author=John%20F.%20Heidelberg,%20Ian%20T.%20Paulsen,%20Karen%20E.%20Nelson,%20Eric%20J.%20Gaidos,%20William%20C.%20Nelson%20et%20al.&contentID=10.1038/nbt749&publicationDate=10/07/2002&volumeNum=20&issueNum=11&numPages=6&pageNumbers=pp1118-1123 site].
*Do the authors own the rights under a Creative Commons license?
**Yes, according to this [http://oaspa.org/member/nature-publishing-group-palgrave-macmillan/ site].
*Is the article available “Open Access”?
**According to [http://oaspa.org/membership/members/ this site], the article is available "Open Access".
*What organization is the publisher of the article? What type of organization is it?
**According to the site above, this publisher is a "Professional OA Publisher (Large)".
*Is this article available in print or online only?
**Online only. It was published online in November, 2002.
*Has LMU paid a subscription or other fee for your access to this article?
**No.
*We performed a search in the ISI Web of Science/Knowledge database by typing in the title "Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis" to the search bar.
**Three articles came up as results. The first two articles title's did not exactly match, and were cited under 15 times each. The third article was the article we were searching for.
*How many articles does this article cite?
**This article has 41 cited references within the Web of Science Core Collection, according to this [https://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=3&SID=3Evs6J6HvCojNOHG6K3&page=1&doc=3 site].
*How many articles cite this article?
**It has been cited 1079 times in all databases, and 426 within the Web of Science Core Collection, according to this [https://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=3&SID=3Evs6J6HvCojNOHG6K3&page=1&doc=3 site].
*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?
**Examples of titles that reference the genome paper:
***Environmental genome shotgun sequencing of the Sargasso Sea
***Deciphering the evolution and metabolism of an anammox bacterium from a community genome
***Genome of Geobacter sulfurreducens: Metal reduction in subsurface environments
***More can be found by clicking this [https://apps.webofknowledge.com/summary.do?product=WOS&parentProduct=UA&search_mode=CitingArticles&qid=8&SID=3Evs6J6HvCojNOHG6K3&page=1&action=sort&sortBy=LC.D;PY.D;AU.A.en;SO.A.en;VL.D;PG.A&showFirstPage=1 link].
**These papers include studying within in the species, finding out the genomes of other species, as well as the metabolic versatility of microorganisms and metal ion reduction in environments. This shows that a sequenced genome can aide in experiments of many kinds.

===Our Microarray Paper===
*Dataset can be found at this [https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15334/?keywords=&organism=Shewanella+oneidensis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= link].


====E-GEOD-15334: Yang et. al (2009)====

This paper is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:41, 10 November 2015 (PST)''

Yang, Y., Harris, D. P., Luo, F., Xiong, W., Joachimiak, M., Wu, L., ... & Zhou, J. (2009). Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. ''BMC genomics, 10''(1), 131.
*The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed/?term=Yang%2C+Y.%2C+Harris%2C+D.+P.%2C+Luo%2C+F.%2C+Xiong%2C+W.%2C+Joachimiak%2C+M.%2C+Wu%2C+L.%2C+...+%26+Zhou%2C+J.+%282009%29.+Snapshot+of+iron+response+in+Shewanella+oneidensis+by+gene+network+reconstruction.+BMC+genomics%2C+10%281%29%2C+131. PubMed].
*The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667191/ PubMedCentral]
*The link to the full text of the article (HTML format) from the publisher [http://www.biomedcentral.com/1471-2164/10/131 web site].
*The link to the full [http://www.biomedcentral.com/content/pdf/1471-2164-10-131.pdf PDF] version of the article from the publisher web site.
*Who owns the rights to the article?
**The article is Open Access and the authors own the rights under a Creative Commons license.
*What organization is the publisher of the article? What type of organization is it?
**BMC Genomics is the publisher, which is a scientific society
*Is this article available in print or online only?
**It is online only
*Has LMU paid a subscription or other fee for your access to this article?
**No
*How many articles does this article cite?
**This paper sites 48 other articles
*How many articles cite this article?
**3
***Roles of UndA and MtrC of ''Shewanella putrefaciens'' W3-18-1 in iron reduction
***Global transcriptional response of ''Caulobacter crescentus'' to iron availability
***Molecular ecological network analysis
*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?
**This article has mostly been used to look at the iron response of other strains or organisms. It may have been used for comparison's sake or to modify the original methodology to fit the new experiment.
*Link to microarray data
**Found it on [https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15334/ ArrayExpress]
**This contains the raw data that we will use for our research
*What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
**Strains of ''Shewanella oneidensis'' were put under iron depletion and repletion conditions. The control would be a regular strain of the organism, while the treatments would be either increasing or decreasing the iron levels.
*Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
**4 biological replicates of each treatment condition were performed

Heavy Metal HaterZ Files

2015-12-15T05:11:56Z

Emilysimso: /* MAPPFinder Documents */ edited screenshot

==All Files==
*All files will be listed here.
*Appropriate way to title files:
**FileName_YYYYMMDD_HMH

===Gene Database===
*[[File:So-Std_HMH_20151214.zip]]

===Initial Flow Chart===
*Initial flow chart for experimental design - [[File:Experimental Design Flow Chart 20151115 HMH.pptx]]

===Journal Club Presentation Power Points===
*Microarray Paper Presentation - [[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]
*Genome Paper Presentation - [[File:GenomePPT_20151123_HMH.pdf]]

===Data Processing Notes from Dr. Dahlquist===
*Page 1 of Notes - [[Media:DrDDataProcessNotes1 20151119 HMH.JPG]]
*Page 2 of Notes - [[Media:DrDDataProcessNotes2 20151119 HMH.JPG]]

===GenMapp Builder===
*[[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]

===Statistical Analysis Excel Sheets===
*Prior to Splitting:
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData 20151206 HMH.xlsx]]
* After splitting, use this one:
*# [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx]]
*Following the splitting, averages taken and ttests done to data sets:
*#[[File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx]]
*#* [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx]]
*#* I made corrections to Emily's file because there are 5408 genes, not 5408. I think that both files have the same results not and you can move on to the next step. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:22, 9 December 2015 (PST)''
*Ready for GenMAPP
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]
* Ranked List from MAPPFinder: [[File:Ranked list from MAPPFinder.PNG]]

===Sanity Check Table===
*[[File:Sanity Check Chart 20151212 HMH.xlsx]]

===MAPPFinder Documents===
*gdb file - [[File:So-Std 20151201special.zip]]
*[[File:ColorSetforExpressionData F60C60 20151210 HMH.gex]]
*GenMAPP with all comparisons - [[File:FilesForComparison AllTrials WithGenMAPP 20151212 ES HMH.gex]]
*Filtered GO terms for increased - [[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.txt]]
*Filtered GO terms for decreased - [[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt]]
*Screenshots showing significant results - [[File:CompiledScreenShots 20151212 HMH.docx]]
*MAPP for Fatty Acid Degradation - [[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation 20151214 HMH.PNG]]
*MAPP for Ribosome - [[File:Ribosomal Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Ribosomal Pathway 20151213 HMH.PNG]]

[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

File:Fatty Acid Degradation 20151214 HMH.PNG

2015-12-15T05:11:11Z

Emilysimso:

File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp

2015-12-15T05:10:23Z

Emilysimso: Emilysimso uploaded a new version of File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp

Emilysimso Week 15

2015-12-14T21:43:31Z

Emilysimso: /* Individual Reflection */ format

==Procedure==
*Calculated averages from split data for each time point and replicate
**Total of 5409 genes
*Calculated biological averages of each time point
*Calculated AverageLogRatio comparing C5, C20, and C60 to C0 and F5, F20, and F60 to C60
**Subtracted not divided due to log space
*Performed TTest on the above relationships to get the Pvalue
*Performed Bonferroni
*Performed Benjamini & Hochberg
*Created new sheet forGenMAPP
**Did adjustments to prepare file for GenMAPP
**Saved as .txt and uploaded to wiki

===GenMAPP===
*Increase criterea = >0.25 AND B-H <0.05
*Decrease criterea <-0.25 AND B-H <0.05
*1441 errors in the raw data
*Red is increased, green is decreased
*Uploaded C5-C0, C20-C0, C60-C0, F5-C60, F20-C60, and F60-C60 into GenMAPP

===MAPPFinder===
*Criteria: Zscore >2, Permute P<0.05, Number Changed > or equal to 4 < or equal to 100, Percent Changed > or equal to 50%

==Files==
*New spreadsheet
**File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx
*Spreadsheet for GenMAPP
**[[File:CompiledRawData WithGenMAPP 20151208 HMH.docx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]

==Individual Reflection==
*Statement of Work
**Describe what you did
**Provide references or links to artifacts of your work (wiki, documents)
*Assessment of Project
**Success of project workflow/teamwork
**What worked and what didn’t?
**What would you do differently?
**Evaluate Gene Database Project and Group Report
**Content: what is the quality?
**Organization
**Completeness: did we reach all objectives
*Reflection on the Process
**What did you learn
***With head (bio or CS principles)
***Heart (qualities, teamwork qualities)
***Hands (technical skills)
**What lesson will you take away

I was a GenMAPP User for the group project, meaning I did the raw data analysis from the microarray experiment and worked with the program to analyze the results. I compiled the data from the repletion stage of the experiment (all of the F time points - found on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_12 Week 12 page]) and then combined this data with Ron to perform the statistical analysis on the data (found on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_14 Week 14 page]). I also created the file we used for [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:UpdatedCompiledRawData_WithGenMAPP_20151210_ES_HMH.xlsx GenMAPP]. I worked with Josh to enter the data into GenMAPP and then worked with Ron to figure out the criteria for significance of the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion0-GO_20151212_HMH.xlsx increased] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion1-GO_20151212_HMH.xlsx decreased] genes. I also created the MAPPs for the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Fatty_Acid_Degradation_Soneidensis_20151213_HMH.mapp Fatty Acid Degradation] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Ribosomal_Soneidensis_20151213_HMH.mapp Ribosome] gene pathways. Finally, I created the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Experimental_Design_Flow_Chart_20151115_HMH.pptx experimental design flow chart].

I think our group worked fairly well together, but we had some issues with communication. Everyone was responsible and got their work done, but sometimes it was unclear when things would be finished or who needed to do which task. There were also some problems with direction and we could have used someone taking a stronger leadership role. I think we should have met more together outside of class to clear up some of these issues, so I would have definitely done that differently. Specifically, Ron and I should have met more to work on the Excel files, since it was unnecessarily complicated doing it apart from each other. Overall, however, I think our group was able to work together to finish the project.

I learned a lot from this project and I think the class as a whole will stay with me beyond undergrad. This course helped solidify the connection between biology and computer science, which is something I had not previously thought much about. I think I learned more about computer science overall, as I had not been exposed to that field before, in terms of database construction, coding, and how various programs can be put together for a final result. In terms of teamwork, this project reminded me how important it is to use people’s skills and work together to make the best project. This project was very specialized, so building off of individual knowledge definitely helped. I think this will help with future projects, especially as they become more involved and specific. For technical skills, I learned how to do some basic coding, database construction, and analysis of a species’ genome. Learning to interpret genomic data is an important skill to start building, as the field is always growing and becoming increasingly relevant to biology.
The biggest lesson I will take away is

{{Template: Esimso entries etc}}

Emilysimso Week 15

2015-12-14T21:43:05Z

Emilysimso: /* Individual Reflection */ added link

==Procedure==
*Calculated averages from split data for each time point and replicate
**Total of 5409 genes
*Calculated biological averages of each time point
*Calculated AverageLogRatio comparing C5, C20, and C60 to C0 and F5, F20, and F60 to C60
**Subtracted not divided due to log space
*Performed TTest on the above relationships to get the Pvalue
*Performed Bonferroni
*Performed Benjamini & Hochberg
*Created new sheet forGenMAPP
**Did adjustments to prepare file for GenMAPP
**Saved as .txt and uploaded to wiki

===GenMAPP===
*Increase criterea = >0.25 AND B-H <0.05
*Decrease criterea <-0.25 AND B-H <0.05
*1441 errors in the raw data
*Red is increased, green is decreased
*Uploaded C5-C0, C20-C0, C60-C0, F5-C60, F20-C60, and F60-C60 into GenMAPP

===MAPPFinder===
*Criteria: Zscore >2, Permute P<0.05, Number Changed > or equal to 4 < or equal to 100, Percent Changed > or equal to 50%

==Files==
*New spreadsheet
**File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx
*Spreadsheet for GenMAPP
**[[File:CompiledRawData WithGenMAPP 20151208 HMH.docx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]

==Individual Reflection==
*Statement of Work
**Describe what you did
**Provide references or links to artifacts of your work (wiki, documents)
*Assessment of Project
**Success of project workflow/teamwork
**What worked and what didn’t?
**What would you do differently?
**Evaluate Gene Database Project and Group Report
**Content: what is the quality?
**Organization
**Completeness: did we reach all objectives
*Reflection on the Process
**What did you learn
***With head (bio or CS principles)
***Heart (qualities, teamwork qualities)
***Hands (technical skills)
**What lesson will you take away

I was a GenMAPP User for the group project, meaning I did the raw data analysis from the microarray experiment and worked with the program to analyze the results. I compiled the data from the repletion stage of the experiment (all of the F time points - found on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_12 Week 12 page]) and then combined this data with Ron to perform the statistical analysis on the data (found on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_14 Week 14 page]. I also created the file we used for [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:UpdatedCompiledRawData_WithGenMAPP_20151210_ES_HMH.xlsx GenMAPP]. I worked with Josh to enter the data into GenMAPP and then worked with Ron to figure out the criteria for significance of the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion0-GO_20151212_HMH.xlsx increased] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion1-GO_20151212_HMH.xlsx decreased] genes. I also created the MAPPs for the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Fatty_Acid_Degradation_Soneidensis_20151213_HMH.mapp Fatty Acid Degradation] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Ribosomal_Soneidensis_20151213_HMH.mapp Ribosome] gene pathways. Finally, I created the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Experimental_Design_Flow_Chart_20151115_HMH.pptx experimental design flow chart].

I think our group worked fairly well together, but we had some issues with communication. Everyone was responsible and got their work done, but sometimes it was unclear when things would be finished or who needed to do which task. There were also some problems with direction and we could have used someone taking a stronger leadership role. I think we should have met more together outside of class to clear up some of these issues, so I would have definitely done that differently. Specifically, Ron and I should have met more to work on the Excel files, since it was unnecessarily complicated doing it apart from each other. Overall, however, I think our group was able to work together to finish the project.

I learned a lot from this project and I think the class as a whole will stay with me beyond undergrad. This course helped solidify the connection between biology and computer science, which is something I had not previously thought much about. I think I learned more about computer science overall, as I had not been exposed to that field before, in terms of database construction, coding, and how various programs can be put together for a final result. In terms of teamwork, this project reminded me how important it is to use people’s skills and work together to make the best project. This project was very specialized, so building off of individual knowledge definitely helped. I think this will help with future projects, especially as they become more involved and specific. For technical skills, I learned how to do some basic coding, database construction, and analysis of a species’ genome. Learning to interpret genomic data is an important skill to start building, as the field is always growing and becoming increasingly relevant to biology.
The biggest lesson I will take away is

{{Template: Esimso entries etc}}

Emilysimso Week 15

2015-12-14T21:41:58Z

Emilysimso: /* Individual Reflection */ formatting

==Procedure==
*Calculated averages from split data for each time point and replicate
**Total of 5409 genes
*Calculated biological averages of each time point
*Calculated AverageLogRatio comparing C5, C20, and C60 to C0 and F5, F20, and F60 to C60
**Subtracted not divided due to log space
*Performed TTest on the above relationships to get the Pvalue
*Performed Bonferroni
*Performed Benjamini & Hochberg
*Created new sheet forGenMAPP
**Did adjustments to prepare file for GenMAPP
**Saved as .txt and uploaded to wiki

===GenMAPP===
*Increase criterea = >0.25 AND B-H <0.05
*Decrease criterea <-0.25 AND B-H <0.05
*1441 errors in the raw data
*Red is increased, green is decreased
*Uploaded C5-C0, C20-C0, C60-C0, F5-C60, F20-C60, and F60-C60 into GenMAPP

===MAPPFinder===
*Criteria: Zscore >2, Permute P<0.05, Number Changed > or equal to 4 < or equal to 100, Percent Changed > or equal to 50%

==Files==
*New spreadsheet
**File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx
*Spreadsheet for GenMAPP
**[[File:CompiledRawData WithGenMAPP 20151208 HMH.docx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]

==Individual Reflection==
*Statement of Work
**Describe what you did
**Provide references or links to artifacts of your work (wiki, documents)
*Assessment of Project
**Success of project workflow/teamwork
**What worked and what didn’t?
**What would you do differently?
**Evaluate Gene Database Project and Group Report
**Content: what is the quality?
**Organization
**Completeness: did we reach all objectives
*Reflection on the Process
**What did you learn
***With head (bio or CS principles)
***Heart (qualities, teamwork qualities)
***Hands (technical skills)
**What lesson will you take away

I was a GenMAPP User for the group project, meaning I did the raw data analysis from the microarray experiment and worked with the program to analyze the results. I compiled the data from the repletion stage of the experiment (all of the F time points - found on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_12 Week 12 page]) and then combined this data with Ron to perform the statistical analysis on the data. I also created the file we used for [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:UpdatedCompiledRawData_WithGenMAPP_20151210_ES_HMH.xlsx GenMAPP]. I also worked with Josh to enter the data into GenMAPP and then worked with Ron to figure out the criteria for significance of the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion0-GO_20151212_HMH.xlsx increased] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion1-GO_20151212_HMH.xlsx decreased] genes. I also created the MAPPs for the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Fatty_Acid_Degradation_Soneidensis_20151213_HMH.mapp Fatty Acid Degradation] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Ribosomal_Soneidensis_20151213_HMH.mapp Ribosome] gene pathways. Finally, I created the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Experimental_Design_Flow_Chart_20151115_HMH.pptx experimental design flow chart].

I think our group worked fairly well together, but we had some issues with communication. Everyone was responsible and got their work done, but sometimes it was unclear when things would be finished or who needed to do which task. There were also some problems with direction and we could have used someone taking a stronger leadership role. I think we should have met more together outside of class to clear up some of these issues, so I would have definitely done that differently. Specifically, Ron and I should have met more to work on the Excel files, since it was unnecessarily complicated doing it apart from each other. Overall, however, I think our group was able to work together to finish the project.

I learned a lot from this project and I think the class as a whole will stay with me beyond undergrad. This course helped solidify the connection between biology and computer science, which is something I had not previously thought much about. I think I learned more about computer science overall, as I had not been exposed to that field before, in terms of database construction, coding, and how various programs can be put together for a final result. In terms of teamwork, this project reminded me how important it is to use people’s skills and work together to make the best project. This project was very specialized, so building off of individual knowledge definitely helped. I think this will help with future projects, especially as they become more involved and specific. For technical skills, I learned how to do some basic coding, database construction, and analysis of a species’ genome. Learning to interpret genomic data is an important skill to start building, as the field is always growing and becoming increasingly relevant to biology.
The biggest lesson I will take away is

{{Template: Esimso entries etc}}

Emilysimso Week 15

2015-12-14T21:39:41Z

Emilysimso: Added individual reflection, added links

==Procedure==
*Calculated averages from split data for each time point and replicate
**Total of 5409 genes
*Calculated biological averages of each time point
*Calculated AverageLogRatio comparing C5, C20, and C60 to C0 and F5, F20, and F60 to C60
**Subtracted not divided due to log space
*Performed TTest on the above relationships to get the Pvalue
*Performed Bonferroni
*Performed Benjamini & Hochberg
*Created new sheet forGenMAPP
**Did adjustments to prepare file for GenMAPP
**Saved as .txt and uploaded to wiki

===GenMAPP===
*Increase criterea = >0.25 AND B-H <0.05
*Decrease criterea <-0.25 AND B-H <0.05
*1441 errors in the raw data
*Red is increased, green is decreased
*Uploaded C5-C0, C20-C0, C60-C0, F5-C60, F20-C60, and F60-C60 into GenMAPP

===MAPPFinder===
*Criteria: Zscore >2, Permute P<0.05, Number Changed > or equal to 4 < or equal to 100, Percent Changed > or equal to 50%

==Files==
*New spreadsheet
**File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx
*Spreadsheet for GenMAPP
**[[File:CompiledRawData WithGenMAPP 20151208 HMH.docx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]

==Individual Reflection==
*Statement of Work
**Describe what you did
**Provide references or links to artifacts of your work (wiki, documents)
*Assessment of Project
**Success of project workflow/teamwork
**What worked and what didn’t?
**What would you do differently?
**Evaluate Gene Database Project and Group Report
**Content: what is the quality?
**Organization
**Completeness: did we reach all objectives
*Reflection on the Process
**What did you learn
***With head (bio or CS principles)
***Heart (qualities, teamwork qualities)
***Hands (technical skills)
**What lesson will you take away

I was a GenMAPP User for the group project, meaning I did the raw data analysis from the microarray experiment and worked with the program to analyze the results. I compiled the data from the repletion stage of the experiment (all of the F time points - found on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_12 | Week 12 page]) and then combined this data with Ron to perform the statistical analysis on the data. I also created the file we used for [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:UpdatedCompiledRawData_WithGenMAPP_20151210_ES_HMH.xlsx GenMAPP]. I also worked with Josh to enter the data into GenMAPP and then worked with Ron to figure out the criteria for significance of the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion0-GO_20151212_HMH.xlsx increased] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion1-GO_20151212_HMH.xlsx decreased] genes. I also created the MAPPs for the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Fatty_Acid_Degradation_Soneidensis_20151213_HMH.mapp Fatty Acid Degradation] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Ribosomal_Soneidensis_20151213_HMH.mapp Ribosome] gene pathways. Finally, I created the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Experimental_Design_Flow_Chart_20151115_HMH.pptx experimental design flow chart].
I think our group worked fairly well together, but we had some issues with communication. Everyone was responsible and got their work done, but sometimes it was unclear when things would be finished or who needed to do which task. I think we should have met more together outside of class to clear up some of these issues, so I would have definitely done that differently. Specifically, Ron and I should have met more to work on the Excel files, since it was unnecessarily complicated doing it apart from each other. Overall, however, I think our group was able to work together to finish the project.
I learned a lot from this project and I think the class as a whole will stay with me beyond undergrad. This course helped solidify the connection between biology and computer science, which is something I had not previously thought much about. I think I learned more about computer science overall, as I had not been exposed to that field before, in terms of database construction, coding, and how various programs can be put together for a final result. In terms of teamwork, this project reminded me how important it is to use people’s skills and work together to make the best project. This project was very specialized, so building off of individual knowledge definitely helped. I think this will help with future projects, especially as they become more involved and specific. For technical skills, I learned how to do some basic coding, database construction, and analysis of a species’ genome. Learning to interpret genomic data is an important skill to start building, as the field is always growing and becoming increasingly relevant to biology.
The biggest lesson I will take away is

{{Template: Esimso entries etc}}

Heavy Metal HaterZ Files

2015-12-14T06:42:32Z

Emilysimso: /* MAPPFinder Documents */ added files

==All Files==
*All files will be listed here.
*Appropriate way to title files:
**FileName_YYYYMMDD_HMH

===Initial Flow Chart===
*Initial flow chart for experimental design - [[File:Experimental Design Flow Chart 20151115 HMH.pptx]]

===Journal Club Presentation Power Points===
*Microarray Paper Presentation - [[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]
*Genome Paper Presentation - [[File:GenomePPT_20151123_HMH.pdf]]

===Data Processing Notes from Dr. Dahlquist===
*Page 1 of Notes - [[Media:DrDDataProcessNotes1 20151119 HMH.JPG]]
*Page 2 of Notes - [[Media:DrDDataProcessNotes2 20151119 HMH.JPG]]

===GenMapp Builder===
*[[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]

===Statistical Analysis Excel Sheets===
*Prior to Splitting:
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData 20151206 HMH.xlsx]]
* After splitting, use this one:
*# [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx]]
*Following the splitting, averages taken and ttests done to data sets:
*#[[File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx]]
*#* [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx]]
*#* I made corrections to Emily's file because there are 5408 genes, not 5408. I think that both files have the same results not and you can move on to the next step. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:22, 9 December 2015 (PST)''
*Ready for GenMAPP
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]
* Ranked List from MAPPFinder: [[File:Ranked list from MAPPFinder.PNG]]

===Sanity Check Table===
*[[File:Sanity Check Chart 20151212 HMH.xlsx]]

===MAPPFinder Documents===
*gdb file - [[File:So-Std 20151201special.zip]]
*[[File:ColorSetforExpressionData F60C60 20151210 HMH.gex]]
*GenMAPP with all comparisons - [[File:FilesForComparison AllTrials WithGenMAPP 20151212 ES HMH.gex]]
*Filtered GO terms for increased - [[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.txt]]
*Filtered GO terms for decreased - [[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt]]
*Screenshots showing significant results - [[File:CompiledScreenShots 20151212 HMH.docx]]
*MAPP for Fatty Acid Degradation - [[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation 20151213 HMH.PNG]]
*MAPP for Ribosome - [[File:Ribosomal Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Ribosomal Pathway 20151213 HMH.PNG]]

[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

File:Ribosomal Pathway 20151213 HMH.PNG

2015-12-14T06:42:19Z

Emilysimso:

File:Fatty Acid Degradation 20151213 HMH.PNG

2015-12-14T06:41:54Z

Emilysimso:

File:Ribosomal Soneidensis 20151213 HMH.mapp

2015-12-14T06:41:25Z

Emilysimso:

File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp

2015-12-14T06:40:34Z

Emilysimso:

File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt

2015-12-13T23:39:02Z

Emilysimso: Emilysimso uploaded a new version of File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt

File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx

2015-12-13T23:38:45Z

Emilysimso: Emilysimso uploaded a new version of File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx

File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.txt

2015-12-13T23:37:26Z

Emilysimso: Emilysimso uploaded a new version of File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.txt

File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx

2015-12-13T23:36:32Z

Emilysimso: Emilysimso uploaded a new version of File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx

Heavy Metal HaterZ Files

2015-12-13T23:30:18Z

Emilysimso: /* MAPPFinder Documents */ added .txt file

==All Files==
*All files will be listed here.
*Appropriate way to title files:
**FileName_YYYYMMDD_HMH

===Initial Flow Chart===
*Initial flow chart for experimental design - [[File:Experimental Design Flow Chart 20151115 HMH.pptx]]

===Journal Club Presentation Power Points===
*Microarray Paper Presentation - [[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]
*Genome Paper Presentation - [[File:GenomePPT_20151123_HMH.pdf]]

===Data Processing Notes from Dr. Dahlquist===
*Page 1 of Notes - [[Media:DrDDataProcessNotes1 20151119 HMH.JPG]]
*Page 2 of Notes - [[Media:DrDDataProcessNotes2 20151119 HMH.JPG]]

===GenMapp Builder===
*[[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]

===Statistical Analysis Excel Sheets===
*Prior to Splitting:
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData 20151206 HMH.xlsx]]
* After splitting, use this one:
*# [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx]]
*Following the splitting, averages taken and ttests done to data sets:
*#[[File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx]]
*#* [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx]]
*#* I made corrections to Emily's file because there are 5408 genes, not 5408. I think that both files have the same results not and you can move on to the next step. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:22, 9 December 2015 (PST)''
*Ready for GenMAPP
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]
* Ranked List from MAPPFinder: [[File:Ranked list from MAPPFinder.PNG]]

===Sanity Check Table===
*[[File:Sanity Check Chart 20151212 HMH.xlsx]]

===MAPPFinder Documents===
*gdb file - [[File:So-Std 20151201special.zip]]
*[[File:ColorSetforExpressionData F60C60 20151210 HMH.gex]]
*GenMAPP with all comparisons - [[File:FilesForComparison AllTrials WithGenMAPP 20151212 ES HMH.gex]]
*Filtered GO terms for increased - [[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.txt]]
*Filtered GO terms for decreased - [[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt]]
*Screenshots showing significant results - [[File:CompiledScreenShots 20151212 HMH.docx]]

[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt

2015-12-13T23:29:48Z

Emilysimso: