Difference between revisions of "Troque Week 10"

Revision as of 01:06, 6 November 2015

Bibliography

Basic search:

• PubMed
  • Original keywords: "shigella flexneri": 4832 results
  • Keyword combinations: "shigella flexneri genome": 5 results, "shigella flexneri 2a": 609 results

• Google Scholar
  • Original keywords: "shigella flexneri": 66,100 results
  • Keyword combinations: "shigella flexneri genome": 27,800 results, "shigella flexneri genome sequence": 25,300 results, "shigella flexneri genome sequence": 21,300 results, "shigella flexneri 2a genome sequence article": 18,100 results,

• Web of science
  • Original keywords: "shigella flexneri": 7408 results
  • Keyword combinations: "shigella flexneri genome": 42, "shigella flexneri genome sequence": 33,

Advanced search:

• PubMed

• Google Scholar
• I, at first, used the "Find articles with all of the words" function, but that didn't help as much since the basic search method already uses this function by default so I ended up with the same results. When I used the "Find articles with the exact phrase" with the phrase "shigella flexneri genome", it only showed me 31 results.

• Web of science
• I mainly used the dropdown list next to the search bar (the one that lists "Topic", "Title", etc.) in order to focus my search.

We ended up with 2 potential genome sequence papers once we entered the title of the article we found on PubMed into the Web of Science database. From WoS, we used the Citation Network feature in order to find the articles that were cited in the paper from PubMed. The paper cited 13 other articles so this seemed like a good enough point to sift through the ones with the actual complete genome sequence for our species.

After all of these, the genome sequence paper that we ended up deciding was the one titled "Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157".

• 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?
         • 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.

Sample Bibliographic Entry

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. Molecular Biology of the Cell, 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
• Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
• Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
• Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article); article is not Open Access, but is freely available 2 months after publication
• Publisher: American Society for Cell Biology (scientific society)
• Availability: in print and online
• Did LMU pay a fee for this article: no