Difference between revisions of "Msaeedi23 Week 10"

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* I narrowed the search down by searching for "complete genome bordetella pertussis" which significantly narrowed the results down to 52.  
 
* I narrowed the search down by searching for "complete genome bordetella pertussis" which significantly narrowed the results down to 52.  
  
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'Use the advanced search functions for each of these three databases/tools and answer the following:'
 
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'''PubMed'''
 
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# Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 
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'''Google Scholar'''
 
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# Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 
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'''Web of Science'''
 
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# Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 
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*#* Each of the references in your bibliography needs to have the following information (an example is given in another section below):
 
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*#** The complete bibliographic reference in the APA style (see the [http://libguides.lmu.edu/c.php?g=324079&p=2174128 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).)
 
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*#** The link to the abstract from  [http://www.ncbi.nlm.nih.gov/pubmed PubMed].
 
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*#** The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].
 
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*#** The link to the full text of the article (HTML format) from the publisher web site.
 
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*#** The link to the full PDF version of the article from the publisher web site.
 
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*#** Who owns the rights to the article?
 
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*#*** Does the journal own the copyright?
 
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*#*** Do the authors own the copyright?
 
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*#*** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license?
 
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*#*** Is the article available “Open Access”?
 
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*#** 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 [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.]
 
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*#** Is this article available in print or online only?
 
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*#** Has LMU paid a subscription or other fee for your access to this article?
 
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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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*#* Give an overview of the results of the search.
 
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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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*#** 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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*# 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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*#* 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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*#** 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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*#** 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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*#** The control sample needs to be derived from mRNA and not genomic DNA.
 
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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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*#* 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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*#* State what you used as search terms and what type of search terms they were.
 
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*#* Give an overview of the results of the search.
 
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*#** How many results did you get?
 
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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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*#* <http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-1871/?keywords=&organism=Bordetella+pertussis&exptype[]=&exptype[]=%22array+assay%22&array=>
 
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*#* <http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29579/?keywords=&organism=Bordetella+pertussis&exptype[]=&exptype[]=%22array+assay%22&array=> click citation link
 
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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?
 
 
*#** Remember, microarray data is not centrally located on the web.  Some major sources are:
 
*#** Remember, microarray data is not centrally located on the web.  Some major sources are:
 
*#*** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] ('''''recommended''''')
 
*#*** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] ('''''recommended''''')
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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.
 
*#* 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.
 
**data for bordetella pertussis <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49385>
 
**data for bordetella pertussis <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49385>
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==Annotated Bibliography==
 +
Genome Sequencing Paper:
 +
 +
King, A. J., van Gorkom, T., Pennings, J. L., van der Heide, H. G., He, Q., Diavatopoulos, D., … Mooi, F. R. (2010). Correction: Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains. BMC Genomics, 11, 196. http://doi.org/10.1186/1471-2164-11-196
 +
 +
* PubMed Abstract:  http://www.biomedcentral.com/1471-2164/9/311#abs
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* PubMed Central: <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481270/>
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* Publisher Full Text (HTML):  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481270/
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* Publisher Full Text (PDF): <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481270/pdf/1471-2164-9-311.pdf>
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* Copyright:  © 2008 King et al; licensee BioMed Central Ltd.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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* Publisher: BMC Genomics
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* Availability: online access
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* Did LMU pay a fee for this article: no
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Microarray Papers:
 +
 +
Nakamura, M. M., Liew, S.-Y., Cummings, C. A., Brinig, M. M., Dieterich, C., & Relman, D. A. (2006). Growth Phase- and Nutrient Limitation-Associated Transcript Abundance Regulation in Bordetella pertussis  . Infection and Immunity, 74(10), 5537–5548. http://doi.org/10.1128/IAI.00781-06
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* PubMed Abstract:  <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1594893/?report=reader#__abstractid499869title>
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* PubMed Central: <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1594893/>
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* Publisher Full Text (HTML): <http://iai.asm.org/content/74/10/5537.full>
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* Publisher Full Text (PDF):  <http://iai.asm.org/content/74/10/5537.full.pdf+html>
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* Copyright: © 2006, American Society for Microbiology
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* Publisher: Infection and Immunity
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* Availability: online access
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* Did LMU pay a fee for this article: no
 +
 +
# What experiment was performed?  What was the "treatment" and what was the "control" in the experiment?
 +
#*Changes in the complete "transcriptional profile" of Bordetella Pertussis was tested using two distinct strains, to determine responses in respective growth phases-lag, log, stationary- and to specific nutrient limitations. GMT-1 and Tohama I were the wild-type clinical isolates used as the control in the experiment. Tahoma I Sc3 mutants were grown from the wild type strain and selected for Bvg+. This is a phase locked mutant derived from a single substitution in bvgS.
 +
#  Were replicate experiments of the "treatment" and "control" conditions conducted?  Were these biological or technical replicates?  How many of each?
 +
#*Tahoma I and Tahoma I Sc3 mutants were plated into 12 separate plates, six of each. Microarray data from previous research analyzing GMT 1 was used to compare transcriptional differences observed in distinct bacterial phases under differing nutrient limitations for both the mutant and wild-type strain.
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 +
{{Template: msaeedi23}}

Latest revision as of 23:49, 10 November 2015

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

<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4463544/> 

What original keyword(s) did you use?  How many results did you get?
  • Searched for "bordetella pertussis" and it produced 9183 results. 
Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
  • Searched for "complete genome bordetella pertussis" and received 2129 results. 
Google Scholar

<http://www.nature.com/ng/journal/v35/n1/abs/ng1227.html> 

What original keyword(s) did you use?  How many results did you get?
  • I searched "bordetella pertussis" and received 69,400 results. 
Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
  • In adding "genome sequence" to my search I was able to narrow down the search results much more. I ended up receiving almost a third of the results at 20,300.
Web of Science

<http://apps.webofknowledge.com/full_record.do?product=WOS&search_mode=GeneralSearch&qid=2&SID=3Elv4Vzh4mOAmjyCxBn&page=1&doc=7> 

What original keyword(s) did you use?  How many results did you get?
  • In the initial search I conducted, I searched for "bordetella pertussis" and received 34,588 results.
Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
  • I narrowed the search down by searching for "complete genome bordetella pertussis" which significantly narrowed the results down to 52.
        • 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.

Annotated Bibliography

Genome Sequencing Paper:

King, A. J., van Gorkom, T., Pennings, J. L., van der Heide, H. G., He, Q., Diavatopoulos, D., … Mooi, F. R. (2010). Correction: Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains. BMC Genomics, 11, 196. http://doi.org/10.1186/1471-2164-11-196

Microarray Papers:

Nakamura, M. M., Liew, S.-Y., Cummings, C. A., Brinig, M. M., Dieterich, C., & Relman, D. A. (2006). Growth Phase- and Nutrient Limitation-Associated Transcript Abundance Regulation in Bordetella pertussis . Infection and Immunity, 74(10), 5537–5548. http://doi.org/10.1128/IAI.00781-06

  1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
    • Changes in the complete "transcriptional profile" of Bordetella Pertussis was tested using two distinct strains, to determine responses in respective growth phases-lag, log, stationary- and to specific nutrient limitations. GMT-1 and Tohama I were the wild-type clinical isolates used as the control in the experiment. Tahoma I Sc3 mutants were grown from the wild type strain and selected for Bvg+. This is a phase locked mutant derived from a single substitution in bvgS.
  2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
    • Tahoma I and Tahoma I Sc3 mutants were plated into 12 separate plates, six of each. Microarray data from previous research analyzing GMT 1 was used to compare transcriptional differences observed in distinct bacterial phases under differing nutrient limitations for both the mutant and wild-type strain.

Mahrad Saeedi

Class Whoopers Team Page
Assignment Links
Individual Journals
Shared Journals
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