Difference between revisions of "Troque Week 10"

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*# Use the genome sequencing article you found to perform a ''prospective'' search in the ISI Web of Science/Knowledge database.
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=== Genome Paper ===
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*#* Give an overview of the results of the search.
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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.
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*#** How many articles does this article cite?
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*#** How many articles cite this article?
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* 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
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*#** 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?
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* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137130/
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*# 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.
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* Publisher Full Text (HTML): http://nar.oxfordjournals.org/content/30/20/4432.full
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*#* 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.
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* Publisher Full Text (PDF): http://nar.oxfordjournals.org/content/30/20/4432.full.pdf+html
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*#** 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).
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* Copyright: 2002 Oxford University Press
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*#** 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).
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* Publisher: Oxford University Press
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*#** The control sample needs to be derived from mRNA and not genomic DNA.
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* Availability: in print and online
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*#** 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).
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* Did LMU pay a fee for this article: no
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*#* 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.
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*How many articles does this article cite? 37
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*#* State what you used as search terms and what type of search terms they were.
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*How many articles cite this article? 303
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*#* Give an overview of the results of the search.
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*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?  
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*#** How many results did you get?
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*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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*#** Give an assessment of how relevant the results were.
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*#* For each article, please provide all of the same information that you provided for the genome article above.
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*#* In addition, you must also link to the web site where the microarray data resides.
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*#** For each of the microarray articles/datasets, answer the following:
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*#**# What experiment was performed?  What was the "treatment" and what was the "control" in the experiment?
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*#**# Were replicate experiments of the "treatment" and "control" conditions conducted?  Were these biological or technical replicates?  How many of each?
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*#** Remember, microarray data is not centrally located on the web.  Some major sources are:
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*#*** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] ('''''recommended''''')
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*#**** Click on the link to "Browse ArrayExpress"
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*#**** Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
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*#*** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
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*#*** [http://smd.princeton.edu/ Stanford Microarray Database]
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*#*** [http://puma.princeton.edu/ PUMAdb (Princeton Microarray Database)]
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*#*** In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
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*#* 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.
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==== Bibliography for Microarray Papers ====
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=== 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.
 
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.
  
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* Did LMU pay a fee for this article: no
 
* Did LMU pay a fee for this article: no
 
* doi: 10.1128/IAI.00537-13
 
* doi: 10.1128/IAI.00537-13
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<br>
 
 
* How many articles does this article cite? 2
 
* How many articles does this article cite? 2
 
* How many articles cite this article? 52
 
* 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?  
 
* 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.
 
* 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.
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==== Genome Paper ====
 
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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.
 
−
 
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* 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
 
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* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137130/
 
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* Publisher Full Text (HTML): http://nar.oxfordjournals.org/content/30/20/4432.full
 
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* Publisher Full Text (PDF): http://nar.oxfordjournals.org/content/30/20/4432.full.pdf+html
 
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* Copyright: 2002 Oxford University Press
 
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* Publisher: Oxford University Press
 
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* Availability: in print and online
 
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* Did LMU pay a fee for this article: no
 
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<br>
 
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*How many articles does this article cite? 37
 
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*How many articles cite this article? 303
 
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*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.
 

Revision as of 07:46, 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, "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".


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.


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.

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