BIOL368/F14:Week 11

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BIOL368: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Wednesday, November 12 at midnight PST (Tuesday night/Wednesday morning). NOTE that the server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00.

Individual Journal Assignment

  • Store this journal entry as "username Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. These links should all be in your personal template; then use the template on your journal entry.
    • Link to your journal entry from your user page.
    • Link back from your journal entry to your user page.
    • Link to this assignment from your journal entry.
    • Don't forget to add the "BIOL368/F14" category to the end of your wiki page.

Finding a Journal Club Article/Microarray Dataset

  • Your task is to find a published microarray dataset with which you will perform your final project in the course and the corresponding article that you will present for Journal Club 3 next week. (You may have completed this task already by working ahead from your Week 10 Assignment. Your microarray dataset must fulfill the following criteria:
    • The data are from a micraorray experiment that measures changes in gene expression (also known as transcription profiling by array).
    • A minimum of three biological replicates have been performed for each condition measured.
    • 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 experiment was performed on one of the following species:
      • Arabidopsis thaliana
      • Chlamydia trachomatis
      • Escherichia coli K12
      • Helicobacter pylori
      • Mycobacterium smegmatis
      • Mycobacterium tuberculosis H37Rv
      • Plasmodium falciparum
      • Pseudomonas aerugenosa
      • Saccharomyces cerevisiae (budding yeast)
      • Salmonella typhimurium
      • Sinorhizobium meliloti
      • Staphylococcus aureus COL
      • Staphylococcus aureus MRSA252
      • Streptococcus pneumoniae
      • Vibrio cholerae
  • Microarray data are not centrally located on the web. Some major sources are:
  • You learned how to use PubMed, GoogleScholar, and Web of Science for your Week 3 Assignment. In this case, it will be likely be easier to search for the data first in one of the databases listed above and then retrieve the article corresponding to the data.
  • You must make a list of up to five potential articles/datasets on your Week 11 journal page by the end of class on Wednesday, November 5. The instructor will notify you as to which article(s) are approved for your Journal Club presentation and final project as soon as possible. For the article that is approved, please provide the following information:
    • The complete bibliographic reference in the APA style (see the Citation Styles LibGuide or 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 copyright of the article? Is it available “Open Access” under an alternative license such as Creative Commons?
    • 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) (Open Access Scholarly Publishers Association Members)
    • Is this article available in print or online only?
    • Provide the link to the dataset page in the corresponding database (e.g., the data page for the article in ArrayExpress).

Preparation for Journal Club 3

In preparation for the Journal Club, each individual will do the following assignment on their individual Week 11 Journal page.

  1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own URL citation.
  2. Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper. Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
    • What is the main result presented in this paper?
    • What is the importance or significance of this work?
    • What were the limitations in previous studies that led them to perform this work?
    • What were the methods used in the study?
      • What samples did they collect and use for the microarray experiment?
      • How many microarray chips did they hybridize in the experiment?
      • Which samples were paired to hybridize on the chip?
      • Which was labeled red (Cy5)? Which was labeled green (Cy3)?
      • How many replicates did they perform of each type?
        • Biological replicates are made from entirely different biological samples.
        • Technical replicates are made when one biological sample is split at a particular stage in the procedure and then carried through to the end of the procedure.
      • What do they say about how they performed each of the steps listed below? (This is the list of steps required to analyze DNA microarray data.)
        1. Quantitate the fluorescence signal in each spot in the microarray image.
          • Typically performed by the scanner software, although third party software packages do exist.
        2. Calculate the ratio of red/green fluorescence
        3. Log(base 2) transform the ratios
        4. Normalize the log ratios on each microarray slide
        5. Normalize the log ratios for a set of slides in an experiment
        6. Perform statistical analysis on the log ratios
        7. Compare individual genes with known data
        8. Look for patterns (expression profiles; clusters) in the data
        9. Perform Gene Ontology term enrichment analysis
        10. Map onto biological pathways
    • Briefly state the result shown in each of the figures and tables.
    • How do the results of this study compare to the results of previous studies (See Discussion).
  3. Upload your completed PowerPoint slides to your journal page by the Week 11 journal deadline (you may make changes before your presentation Wednesday afternoon, but I will be evaluating the presentation you upload.)

Note: The individual journal entry for this week is worth 10 points like all other journal entries. The journal club presentation is worth 80 points.

Shared Journal Assignment

  • Store your journal entry in the shared BIOL368/F14:Class Journal Week 11 page. If this page does not exist yet, go ahead and create it.
  • Link to the shared journal entry from your user page; this should be part of your template.
  • Link the shared journal page to this assignment page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL368/F14" category to the end of the wiki page (if someone has not already done so).


Often, research is classfied as either hypothesis-driven research or discovery-driven research (where research is conducted without having a prior hypothesis as to the results). For each of the papers that you have read for journal club this semester, answer the following:

  1. Classify each paper as hypothesis-driven or discovery-driven and explain why you gave it this designation.
  2. What do you see are the advantages and disadvantages to each kind of research?