Troque Week 10

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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, "shigella flexneri genome cy3 cy5": 708 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. (Note: these were the results when searching the terms anywhere in the article.
    • What worked best for me would have to be switching the option to look for the terms "anywhere in the article" to "in the title of the article". When I used both "Find articles with all of the words" with this, I only received 29 results, which was the lowest I've received from Google Scholar.
  • 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. 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?
    2. 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:
      • 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.

Bibliography for Microarray Papers

Morris, Carolyn R, et al. ‘Characterization of Intracellular Growth Regulator IcgR by Utilizing Transcriptomics to Identify Mediators of Pathogenesis in Shigella Flexneri’. Infection and Immunity 81.9 (Sep. 2013): 3068–3076. 6 Nov. 2015.


  • How many articles does this article cite? 2
  • How many articles cite this article? 52
  • 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?
  • Since the organism's genome has been sequenced, new research about this specie now tends to focus more on its pathogenesis using bioinformatic methods with in vitro and in vivo microarray data. For example, the article "Analysis of the Proteome of Intracellular Shigella flexneri Reveals Pathways Important for Intracellular Growth" that cites this article analyzes the metabolic pathways that allow the organism to grow.

Genome Paper

Jin, Q., et al. (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.


  • 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.
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