Eyanosch Week 10

From LMU BioDB 2015
Revision as of 06:58, 6 November 2015 by Eyanosch (Talk | contribs)

Jump to: navigation, search

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

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.


          • 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:

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. 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


    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:
      • 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.
Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Eyanosch_Week_10&oldid=5690"