Heavy Metal HaterZ

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Shewanella oneidensis

Our Gene Database Testing Report

Group Paper - File:Final Report 20151218 2 HMH.docx

Group Members

Important Links

Our Files

Our Deliverables

Gene Database Project Links
Overview Deliverables Reference Format Guilds Project Manager GenMAPP User Quality Assurance Coder
Teams Heavy Metal HaterZ The Class Whoopers GÉNialOMICS Oregon Trail Survivors
Individual Journal Entries
Mary Alverson Week 11 Week 12 Week 14 Week 15
Emily Simso Week 11 Week 12 Week 14 Week 15
Ron Legaspi Week 11 Week 12 Week 14 Week 15
Josh Kuroda Week 11 Week 12 Week 14 Week 15

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

  1. What worked?
  2. What didn't work?
  3. What will I do next to fix what didn't work?
  • Mary:
    1. Dr.Dionisio's instructions were very clear so I was able to customize the genMappBuilder and it is working like it should.
    2. 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.
    3. 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:
    1. Our customized export seemed to work, since we got the 4196 count for Ordered Locus Names for which we were looking.
    2. 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.
    3. 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
    1. 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.
    2. 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.
    3. I will redo the Pvalues and the two adjustment calculations. Then I will get the data ready for GenMAPP.
  • Ron
    1. Dr. Dahlquist's instructions and feedback helped with ensuring the manipulation of the data was done accurately.
    2. 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.
    3. 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

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. 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 abstract from PubMed.
  • The full text of the article in PubMedCentral : Not available.
  • The full text of the article from the publisher web site.
  • The 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 site.
  • Do the authors own the rights under a Creative Commons license?
    • Yes, according to this site.
  • Is the article available “Open Access”?
    • According to 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 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 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 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 link.

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

This paper is suitable for your project. — 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 PubMed.
  • The link to the full text of the article in PubMedCentral
  • The link to the full text of the article (HTML format) from the publisher web site.
  • The link to the full 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 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


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