Difference between revisions of "Eyanosch Week 10"

Revision as of 06:58, 6 November 2015

Website to genome sequence papers

http://iai.asm.org/content/69/5/3271.short

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033240 Check out who cited the paper and what articles the paper cited from

http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/?keywords=Shigella+flexneri&organism=Shigella+flexneri&exptype[]=%22rna+assay%22&exptype[]=%22array+assay%22&array=

• Look under files, and use sample and data relationship, raw data, processed data, array design. ETC

Microarray : http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12535

Individual Journal Assignment

• Store this journal entry as "username Week 10" (i.e., this is the text to place between the square brackets when you link to this page).
• Link from your user page to this Assignment page.
• Link to your journal entry from your user page.
• Link back from your journal entry to your user page.
• Don't forget to add the "Journal Entry" category to the end of your wiki page.
  • Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.
• For your assignment this week, you will keep an electronic laboratory notebook on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

Note that each person will complete an individual annotated bibliography. Information from each team member's bibliography will then be compiled on your team's page. This will require coordination among the team members so that both the individual and team assignment will be completed by the journal deadline.

Annotated Bibliography of Genomics Papers for your Species

For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.

• On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
• On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography. Specifically, you need to search the literature/biological databases for the following:
  1. The journal article which describes the results of the whole genome sequencing for your species. (Note that you will be giving a journal club presentation on this article for your Week 11 assignment.)
     • Use a keyword search for each of these databases/tools and answer the following:
       • PubMed
         • What original keyword(s) did you use? How many results did you get?
         • The keywords used were 'shigella flexneri' and that produced 4832 results
         • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
         • To narrow the search down, tags such as 'genome' and 'genome sequencing' were used. The results were narrowed to 664 and 56 respectively.
       • Google Scholar
         • What original keyword(s) did you use? How many results did you get?
         • The keywords used were 'shigella flexneri' and that produced 66,100 results
         • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
         • To narrow the search down, tags such as 'genome' and 'genome sequencing' were used. The results were narrowed to 27,800 and 25,200
       • Web of Science
         • What original keyword(s) did you use? How many results did you get?
         • The keywords used were 'shigella flexneri' and that produced 24,737 results
         • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
         • To narrow the search down, tags such as 'genome' and 'genome sequencing' were used. The results were narrowed to 590 and 460
     • Use the advanced search functions for each of these three databases/tools and answer the following:
       • PubMed
         • Which advanced search functions were most useful to narrow down the search? How many results did you get?
         • Utilizing advanced search functions of publication dates ranging back 5 or 10 years and text availability
       • Google Scholar
         • Which advanced search functions were most useful to narrow down the search? How many results did you get?
         • The advanced options of including patents or citations, by unchecking the boxes narrows the search results down. The results can be sorted by relevance and sorted by date.
       • Web of Science
         • Which advanced search functions were most useful to narrow down the search? How many results did you get?
         • Changing the publication dates to show the order from oldest to newest. Checking the times the article has been cited and the citations of other articles within the chosen article. There are some options within research domain that will help narrow down the search results.

• 1. • Each of the references in your bibliography needs to have the following information (an example is given in another section below):
       • The complete bibliographic reference in the APA style (see the Writing LibGuide) You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
       • 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?

• 1. • • • Does the journal own the copyright?
         • Do the authors own the copyright?
         • Do the authors own the rights under a Creative Commons license?
         • Is the article available “Open Access”?
       • What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization, see the list of) (Open Access Scholarly Publishers Association Members) here.
       • Is this article available in print or online only?
       • Has LMU paid a subscription or other fee for your access to this article?
  2. Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
     • Give an overview of the results of the search.
       • How many articles does this article cite?
       • How many articles cite this article?
       • 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?
  3. Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four articles, please let the instructors know right away.
     • The experiments must be measuring gene expression aka transcriptional profiling or transcription profiling by array. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
       • A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
       • The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
       • The control sample needs to be derived from mRNA and not genomic DNA.
       • The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
     • We recommend that you begin by searching for the data, and then by finding the journal article related to the data. State which database you used to find the data and article.
     • State what you used as search terms and what type of search terms they were.
     • Give an overview of the results of the search.
       • How many results did you get?
       • Give an assessment of how relevant the results were.
     • For each article, please provide all of the same information that you provided for the genome article above.
     • In addition, you must also link to the web site where the microarray data resides.
       • For each of the microarray articles/datasets, answer the following:
         1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
         2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
       • Remember, microarray data is not centrally located on the web. Some major sources are:
         • EBI ArrayExpress (recommended)
           • Click on the link to "Browse ArrayExpress"
           • Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
         • NCBI GEO
         • Stanford Microarray Database
         • PUMAdb (Princeton Microarray Database)
         • In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
     • On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

Bibliographic Entry

Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., … Yu, J. (2002). Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Research, 30(20), 4432–4441.

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+Shigella+flexneri+2a%3A+insights+into+pathogenicity+through+comparison+with+genomes+of+Escherichia+coli+K12+and+O157
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137130/
• Publisher Full Text (HTML): http://nar.oxfordjournals.org/content/30/20/4432.full
• Publisher Full Text (PDF): http://nar.oxfordjournals.org/content/30/20/4432.full.pdf+html
• Copyright: 2002 Oxford University Press
• Publisher: Oxford University Press
• Availability: in print and online
• Did LMU pay a fee for this article: no

• 1. • • • The publisher of the article Oxford University Press is apart of the University of Oxford and its purpose is to advance education and scientific research by publishing worldwide.
       • Is this article available in print or online only?
         • The article is available in both print and online
       • Has LMU paid a subscription or other fee for your access to this article?
         • No LMU has not paid a subscription for access to this article.
       • Used the genome sequencing article to perform a prospective search in the ISI Web of Science/Knowledge database.
• Overview of the search:
  • How many articles does this article cite? 37
  • How many articles cite this article? 303
  • 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?
    • Now that the genome has been sequenced, a majority of research has been done on discovering which genes are responsible for virulence and pathogenesis as well as potential antibiotics. Genomic research is also focused on how S. flexneri has been able to develop resistance to multiple drugs. Furthermore, Shigella is suspected to have evolved from Escherichia coli so a lot of research has been done in how and when pathogenic Shigella split from E. coli on the evolutionary tree.

• 1. Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four articles, please let the instructors know right away.
     • The experiments must be measuring gene expression aka transcriptional profiling or transcription profiling by array. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
       • A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
         • This micro array data provides 6 biological replicates.
       • The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
       • The control sample is derived from mRNA and not genomic DNA.
       • The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
     • The database used to find the micro array was the NCBI Gene Expression Omnibus
     • State what you used as search terms and what type of search terms they were.
       • We used the specific species of shigella flexneri 2a.
     • Give an overview of the results of the search.
       • How many results did you get?
       • 5 results appeared
       • Give an assessment of how relevant the results were.
       • There were 2, possibly 3, relevant restults.
     • For each article, please provide all of the same information that you provided for the genome article above.
     • Micro Array resides:
       • http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12535
       • For each of the microarray articles/datasets, answer the following:
         1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?

A virulence Plasmid cured Shigella flexneri and a wild type shigella flexneri 2a were both observed to see protein expression at 30°C and 37°C. The control would be the Wild type shigella flexneri 2a, and the treatment is the change in temperatures.

• 1. • • 1. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?

There were 12 biological replicates and 4 technical replicates of the experiment done.

Global analysis of a plasmid-cured Shigella flexneri strain: new insights into the interaction between the chromosome and a virulence plasmid. Li Zhu, Xiankai Liu, Xuexue Zheng, Xin Bu, Ge Zhao, Chaohua Xie, Jingfei Zhang, Na Li, Erling Feng, Jie Wang, Yongqiang Jiang, Peitang Huang, Hengliang Wang J Proteome Res. 2010 February 5; 9(2): 843–854. doi: 10.1021/pr9007514

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed?LinkName=gds_pubmed&from_uid=200012535
• PubMed Central: N/A
• Publisher Full Text (HTML): http://pubs.acs.org/doi/full/10.1021/pr9007514
• Publisher Full Text (PDF): http://pubs.acs.org/doi/pdf/10.1021/pr9007514
• Copyright: 2009 American Chemical Society
• Publisher: Journal of Proteome Research
• Availability: in print and online
• Did LMU pay a fee for this article: no

• 1. • • What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization, see the list of) (Open Access Scholarly Publishers Association Members) here.
       • Is this article available in print or online only?
       • Has LMU paid a subscription or other fee for your access to this article?
  2. Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
     • Give an overview of the results of the search.
       • How many articles does this article cite?
       • How many articles cite this article?
       • 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?
  3. Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four articles, please let the instructors know right away.
     • The experiments must be measuring gene expression aka transcriptional profiling or transcription profiling by array. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
       • A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
       • The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
       • The control sample needs to be derived from mRNA and not genomic DNA.
       • The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
     • We recommend that you begin by searching for the data, and then by finding the journal article related to the data. State which database you used to find the data and article.
     • State what you used as search terms and what type of search terms they were.
     • Give an overview of the results of the search.
       • How many results did you get?
       • Give an assessment of how relevant the results were.
     • For each article, please provide all of the same information that you provided for the genome article above.
     • In addition, you must also link to the web site where the microarray data resides.
       • For each of the microarray articles/datasets, answer the following:
         1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
         2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
       • Remember, microarray data is not centrally located on the web. Some major sources are:
         • EBI ArrayExpress (recommended)
           • Click on the link to "Browse ArrayExpress"
           • Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
         • NCBI GEO
         • Stanford Microarray Database
         • PUMAdb (Princeton Microarray Database)
         • In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
     • On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.