Mdoyle Week 7

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BIOL 367 Presentation - GenMAPP 2


Contents

Vocabulary

- 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. 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.

microarray: A tool used to sift through and analyze the information contained within a genome. A microarray consists of different nucleic acid probes that are chemically attached to a substrate, which can be a microchip, a glass slide or a microsphere-sized bead. (http://www.medterms.com/script/main/art.asp?articlekey=30712)

pathway: A sequence of enzymatic or other reactions by which one biological material is converted to another. (http://www.answers.com/topic/pathway)

high-throughput: Automated processes of biological, biochemical or biophysical assay that examine very large numbers of compounds (or compound mixtures) on a short time scale, and enable active compounds to be rapidly identified. (www.medscape.com/viewarticle/502816_sidebar1)

biological assay: Bioassay (commonly used shorthand for biological assay), or biological standardisation is a type of scientific experiment. (en.wikipedia.org/wiki/Biological_assay)

gene ontology: The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species (en.wikipedia.org/wiki/Gene_Ontology)

genomic amplifications: A cellular process characterized by the production of multiple copies of a particular gene or genes to amplify the phenotype that the gene confers on the cell. (http://www.answers.com/topic/gene-amplification)

prostaglandin: a potent substance that acts like a hormone and is found in many bodily tissues (and especially in semen); produced in response to trauma and may affect blood pressure and metabolism and smooth muscle activity (wordnetweb.princeton.edu/perl/webwn)

dearth: an acute insufficiency (wordnetweb.princeton.edu/perl/webwn)

monoamine: a molecule containing one amine group (especially one that is a neurotransmitter) (wordnetweb.princeton.edu/perl/webwn)

myocardial: myocardium - the middle muscular layer of the heart wall (wordnetweb.princeton.edu/perl/webwn)

What is the main result presented in this paper?

    • the development of GenMAPP allows biologists to easily analyze genomic data as a result of its user-friendly interface.

What is the importance or significance of this work?

    • improves the original GenMAPP by providing 3 changes:
      • user data import and mapping are now built-in features
      • “expanded pathway resources”
      • high-throughput biological assays now have increased support
    • this improved version allows for more complex analysis of data as a result, enabling biologists

What were the limitations in previous studies that led them to perform this work?

    • only a few species were supported, ie. human, mouse, rat and yeast
    • only allowed access to a few gene ID systems, ie GenBank, SGD, and UniProt
    • scientists couldn’t view multiple criteria simultaneously
    • pathway information is not typically available for the recently added species

What were the methods used in the study?

    • Windows based operating system
    • implemented in Visual Basic 6.0
    • files stored in Microsoft Jet format

3 major data file types:

  • experimental data - .gex; stores user-uploaded data and custom color criteria
  • gene databases - .gdb; contain gene annotation that is specific to each species from public resources
  • pathways - .mapp; contain a set set of gene or protein identifiers, and can also contain data regarding the author and any relevant literature

major functions of the application include:

  • improved support of genes and species
  • better visualization tools
  • an export functions that makes sharing easier
  • expanded pathway curation
  • the ability to create homology MAPPs
  • improved analysis of pathways - which include gene expression time-point analysis, whole-genome exon array analysis, polymorphism analysis, and proteomic and gene expression analysis

Briefly state the result shown in each of the figures and tables.

    • fig 5: this is an example of how the simultaneous comparison function of GenMAPP works, and it allows the user to compare differences in data over time
    • fig 1: demonstration of the homology mapping function, based on human pathways
    • fig 2: representation of the cut-off for homology MAPPs and the conversion rates for certain species
    • fig 3: comparison of the number of mouse genes shown on GenMAPP versus Gene Ontology
    • fig 4: example of GenMAPP’s ability to pull data from extended pathways
    • fig 5: GenMAPP can do multiple time-point analyses, as evidenced by this example with mouse data
    • fig 6: GenMAPP is also capable of producing visualizations that compare multiple data types, which allows biologists a lot more control over their data analysis
    • table 1: provides information on the number and kind of species supported with GenMAPP, with info also given regarding homology, whether it was contributed and KEGG converted.

How do the results of this study compare to the results of previous studies.

    • GenMAPP 2 still faces a few obstacles, to which it appears improvements to the program are still being worked on.Margie Doyle 02:55, 18 October 2010 (EDT)
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