View source for Heavy Metal HaterZ

{{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

==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.
<!--Accidentally uploaded the ppt guidlines instead of own ppt slides at first. This was noticed and corrected 11/23/2015-->
*[[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 HTML version was not available.)
** I am not sure what you mean by the HTML version not being available.  This link '''''is''''' to the HTML version.  ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:19, 10 November 2015 (PST)''-->
*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].
<!-- *The beginning of the headers given to the bibliography entries correspond to the data set results found when clicking the above link.
** It would have been better to give a direct link to the actual dataset page for each reference below.  Instead, I had to wade through the search results to find each paper/dataset to which you were referring.  ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:47, 10 November 2015 (PST)''

====E-GEOD-15657: Charania et. al (2009)====

This paper is not suitable because they only do two replicates for each condition and we will not be able to do statistics.  ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:40, 10 November 2015 (PST)''

Charania, M. A., Brockman, K. L., Zhang, Y., Banerjee, A., Pinchuk, G. E., Fredrickson, J. K., Beliaev, A.S., Saffarini, D. A. (2009). Involvement of a Membrane-Bound Class III Adenylate Cyclase in Regulation of Anaerobic Respiration in Shewanella oneidensis MR-1 . Journal of Bacteriology, 191(13), 4298–4306. http://doi.org/10.1128/JB.01829-08
* Link to abstract on [http://www.ncbi.nlm.nih.gov/pubmed/?term=Involvement+of+a+membrane-bound+class+III+adenylate+cyclase+in+regulation+of+anaerobic+respiration+in+Shewanella+oneidensis+MR-1. '''PubMed''']
* Link to full text of article on [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2698484/ '''PMC''']
* Link to [http://jb.asm.org/content/191/13/4298.full '''Full Text'''] from publisher.
* Link to [http://jb.asm.org/content/191/13/4298.full.pdf+html '''PDF Version'''] from publisher.
* The American Society for Microbiology owns the copyright. The article is not open-access.
* The publisher is the American Society for Microbiology. It is a scientific society.
* This article is available in the printed and on-line journals.
* LMU has not paid for my access.
* This article has '''39''' citations.
* According to the ''Web of Science'', this article is cited by '''29''' other articles.
* Looking at the titles of the other articles/abstracts, it seems like most research has been focused on catabolic and regulatory pathways of ''Shewanella oneidensis'', along with the two-component system that regulates nitrogen (nitrite and nitrate) respiration.
* Link to [https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-15657/E-GEOD-15657.raw.1.zip '''Raw microarray data''']
* Link to [https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-15657/E-GEOD-15657.processed.1.zip '''Processed microarray data''']
* The experiment looked to find more information about the cyclic AMP receptor protein (CRP) within the membranes of ''Shewanella oneidensis'' that regulates the respiration of fumarate, dimethyl sulfoxide (DMSO), or Fe(III); thus, manipulation of the particular genes were done in order to observe how gene deletions would affect the anaerobic respiration.
* A total of six expression profiles of ''Shewanella oneidensis'' samples (wild-type and mutant strains); 2 wild-type, 2 CRP deletion mutants, cyaC deletion mutants.

====E-GEOD-21044: Lassak et. al (2010)====

This paper is not suitable because they do not use two-color microarray chips.  ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:41, 10 November 2015 (PST)''

Lassak J, Henche AL, Binnenkade L, Thormann KM. (2010). ArcS is the cognate sensor kinase in an atypical Arc system of Shewanella oneidensis MR-1. ''Applied and Environmental Microbiology'', 76(10), 3263-3274.
* [http://www.ncbi.nlm.nih.gov/pubmed/?term=ArcS+is+the+cognate+sensor+kinase+in+an+atypical+Arc+system+of+Shewanella+oneidensis+MR-1 '''PubMed''']
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869118/ '''PMC''']
* [http://aem.asm.org/content/76/10/3263.full '''Full Text''']
* [http://aem.asm.org/content/76/10/3263.full.pdf+html '''PDF Version''']
* The American Society for Microbiology owns the copyright. The article is not open-access.
* The publisher is the American Society for Microbiology. It is a scientific society.
* This article is available in the printed and on-line journals.
* LMU has not paid for my access.
* This article has 76 citations.
* According to the ''Web of Science'', this article is cited by 35 other articles.
* Looking at the titles of the other articles, it seems like most research has been focused on a two-component system present in shewanella oneidensis as well as anaerobic and aerobic respiration.
* [https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-21044/E-GEOD-21044.raw.1.zip '''Raw microarray data''']
* [https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-21044/E-GEOD-21044.processed.1.zip '''Processed microarray data''']
* The experiment looked to find more information about the Arc two-component system of shewanella oneidensis by shifting oxygen levels. The treatment in the experiment was the changing levels of oxygen.  The control were strains of shewanella oneidensis MR-1 wild type cells.
* Expression profiles of three independent replicates of Shewanella oneidensis MR-1 delta-arcS were compared to three independent replicates of Shewanella oneidensis MR-1 wild type cells. -->

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

This paper is suitable for your project.  ''&mdash; [[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

<!-- ===Ranking of Microarray Papers===
#Yang et. al (2009)
#Lassak et. al (2010)
#Charania et. al (2009)

It would have been useful if you had actually numbered the papers and put them in this order above.  I actually looked at them in the order you displayed them above before I scrolled down the page and saw this.  ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:45, 10 November 2015 (PST)'' -->