Evan Montz Week 7: Difference between revisions
Evan Montz (talk | contribs) (Addition of Outline) |
Evan Montz (talk | contribs) (Powerpoint link and signature) |
||
Line 81: | Line 81: | ||
***MAPPFinder is capable of yielding important statistical data such as up regulation, down regulation, and z-scores | ***MAPPFinder is capable of yielding important statistical data such as up regulation, down regulation, and z-scores | ||
==Powerpoint Link== | |||
[[Media: MAPPFinder_Powerpoint.ppt | MAPPFinder Powerpoint]] | |||
[[User:Evan Montz|Evan Montz]] 02:54, 18 October 2010 (EDT) | |||
[[Category:BIOL367/F10]] | [[Category:BIOL367/F10]] |
Latest revision as of 23:54, 17 October 2010
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.
http://en.mimi.hu/biology/gene_expression.html
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.
http://medical-dictionary.thefreedictionary.com/morphogenesis
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.
http://www.merriam-webster.com/medical/hexokinase
4. Directed acyclic graph- A directed graph with no path that starts and ends at the same vertex.
http://xw2k.nist.gov/dads//HTML/directAcycGraph.html
5. Ontology- A branch of metaphysics concerned with the nature and relations of being.
http://www.merriam-webster.com/dictionary/ontology
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.
http://www.merriam-webster.com/medical/spliceosome?show=0&t=1287369260
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.
http://www.yeastgenome.org/cgi-bin/GO/goTerm.pl?goid=0000080
8. Protein biosynthesis- The process in which cells build proteins.
http://www.wordiq.com/definition/Protein_biosynthesis
9. TGFβ signaling- the prototype of a large family of secreted peptide growth factors in metazoans.
http://www.wormbook.org/chapters/www_tgfbsignal/tgfbsignal.html
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.
http://dictionary.reference.com/browse/glycolysis
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
- 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
Powerpoint Link
Evan Montz 02:54, 18 October 2010 (EDT)