Chlamydia trachomatis

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

Contents

Deadlines and Intermediate Milestones

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

THANKSGIVING BREAK

11/28

THANKSGIVING BREAK

11/29

THANKSGIVING BREAK

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

Deliverable and Final Paper Assignments

Deliverables

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

Final Paper

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

Annotated Bibliography of Genomics Papers for C. trachomatis

Whole genome sequencing of C. trachomatis

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

Microarray articles

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

The following articles appear in order of preference:

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

Journal Club Presentation on C. trachomatis Genome Sequencing Paper

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

Important Files

GO OBO-XML file for C. trachomatis serovar A.
UniProt XML file for C. trachomatis serovar A.
GOA file for C. trachomatis serovar A.
First iteration of the export/import gene database cycle.
Updated gene database.
New gene database created with the new version of gmbuilder built on 11/21/2013 using the custom species profile for C. trachomatis.

Array Express Article Raw Files

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

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

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

For GenMAPP Files

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

MAPPFinder Files

Increased
Deceased
File created by MAPPFinder after creating the latest color set.

Final Excel Spreadsheet Containing Everything from GenMAPP and MAPPFinder

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

Wiki Formatting

Template: Template:Team_H(oo)KD

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