Evan Montz Week 7

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10 Biological Term Definitions

1. Gene expression- The process by which the inheritable information in a gene, such as the DNA sequence, is made into a functional gene product, such as protein or RNA.


2. Morphogenesis- Differentiation of cells and tissues in the early embryo which resultsin establishing the form and structure of the various organs and parts of the body.


3. Hexokinase- Any group of enzymes that accelerate the phosphorylation of hexoses (as in the formation of glucose-6-phosphate from glucose and ATP) in carbohydrate metabolism.


4. Directed acyclic graph- A directed graph with no path that starts and ends at the same vertex.


5. Ontology- A branch of metaphysics concerned with the nature and relations of being.


6. Spliceosome- A ribonucleoprotein complex that is the site in the cell nucleus where introns are excised from precursor messenger RNA and exons are joined together to form functional messenger RNA.


7. Mitotic cell cycle- A mitotic cell cycle is one which canonically comprises four successive phases and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells.


8. Protein biosynthesis- The process in which cells build proteins.


9. TGFβ signaling- the prototype of a large family of secreted peptide growth factors in metazoans.


10. Glycolysis- the catabolism of carbohydrates, as glucose and glycogen, by enzymes, with the release of energy and the production of lactic or pyruvic acid.


Outline: MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data

  • Outline
    • MAPPFinder is a tool that has the capability of organizing genes according to their GO identification and is able to compare to other GO terms
      • MAPPFinder integrates the Gene Ontology (GO) Project with GenMAPP
      • Capable of comparing an experimental GO term to a control term
      • Rapidly Generates a graphical representation of thousands of genes in their representative pathways as well as how they are regulated
    • No tool prior to MAPPFinder could link gene term expression data to the Gene Ontology hierarchy.
      • MAPPFinder can be effectively used in combination with GenMAPP, a gene pathway profiler
      • It was determined that pathway profiling should be an automated process in order to quickly explore all possible pathways.
      • GenMAPP currently utilizes 50 MAPPs (Microarray Pathway Profiles)
        • This is insufficient to manage all species
      • MAPPFinder was created in order to interconnect the GenMAPP and GO Project and to quickly compare their contents and to utilize the information provided by both sources
    • The GO consortium consists of a created list of formal biological definitions
      • Definitions include biological processes, cellular components, and molecular functions
      • MAPPFinder calculates percentage of genes measured that match the criterion of the user.
      • Using this percentage in conjunctions with a z-score, MAPPFinder can rank the GO terms by amounts of change in gene expression in comparison to the control
        • A z-score is a rating of confidence that considers whether the change was by chance or not
        • Also determines whether data is up regulated or down regulated.
    • Figure 1: How MAPPFinder Works
      • Figure graphically demonstrates the process that MAPPFinder goes through in order to identify GO terms and use GenMAPP to graphically display data
    • Article performed and example case to demonstrate the advantages of MAPPFinder and how it can be used
      • The example analyzed publicly available mouse microarray data on cardiac development in 12.5 day old mouse embryo and compared it to adult mouse heart cells as the control
      • Program automatically locates genes from microarray and finds the GO terms that are associated with those genes
    • Table 1: Genes found by MAPPFinder
      • Gives data on the amount of genes measured, and more data indicating what database source the genes came from.
      • Yields amount of genes that are known to be associated with the biological processes, cellular components, as well as the molecular function.
      • Also displays amount of genes changed and whether they increased or decreased
    • Table 2: Text representation of showing MAPPFinder results
      • Displays a text version of the data that shows all genes significantly increased and separates the genes by processes, components, and functions.
      • Gives values of percent present, percent changed and a z-score
    • Figure 2: Graphical representation of the MAPPFinder data in the MAPPFinder browser
      • Demonstrates how MAPPFinder uses GO data and graphically displays them
    • Figure 3a: Shows how different pathways can be simply clicked and demonstrate the child terms associated with them
    • Figure 3b
      • Shows graphical representation of what information is seen when a child term is clicked on
    • Figure 3c
      • Demonstrates the graphical representation of Figure 3b when coupled with GenMAPP software
    • MAPPFinder key results from example
      • Highest up regulation was found in cell division and growth pathways
      • Highest down regulation was found in energy metabolism
      • Global view of gene expression changes allow to be put into the context of other regulatory and developmental processes
    • MAPPFinder navigation functions
      • Capable of searching for exact GO term matches
      • Can also search by gene identifier to find GO terms
      • User can also search GO tree to automatically show all nodes that fit the requirement of a minimum number of genes, minimum percent of genes meeting criterion, or minimum z-score
    • Conclusion
      • MAPPFinder is an extremely effective tool that is capable of rapidly comparing microarray data to create a global gene expression profile
      • MAPPFinder is capable of yielding important statistical data such as up regulation, down regulation, and z-scores

Powerpoint Link

MAPPFinder Powerpoint

Evan Montz 02:54, 18 October 2010 (EDT)