Notes taken on week 7

Lecture notes 10/12/10

• Biological pathways
• metabolic- breakdown of molecules
• signaling- transmission of info. from outside to inside the cell
• Gene regulatory- controls gene activity
• these pathways create functional modules, that make up the large scale organization of the cell (universality). These universal traits, found through the organisms genome, can lead to mathematical modeling for the cell's reaction to the environment.

Microarray technology

• red/green ratio = (signal-background red)/(signal-background green)
• determines what genes are turned on/off. This can help in determining genetic pathways.
• Up regulation (>1) vs. down regulation (<1)
• log2 ratios taken of these numbers is necessary to determine magnitude difference, and reduces the outliers.
• Normalization- evens out florescence intensity for an within chips/entire chip/whole experiments.
• Statistical analysis- determines the confidence level of the results (expressed in a P value < 0.05, this is the difference in the data due to chance)
• multiple testing problem- with enough statistical test are performed, there will be significant variations in the data due to chance. Bonferroni correction - multiples the P value by the number of tests, if it is < 0.05 it passes.

GenMAPP

• program that maps biological data from a microarray database into pathway diagrams.
• Gene ontology- allows for a categorization of the data into terms that are ranked based upon the groups functions (MAPPFinder)

XMLpipeDB

• Takes in data from uniprot and gene databases, and creates a GenMAPP gene database. DNA microarray data, analyzed through MAPPFinder. Combining this knowledge, we can discover new results that the original research did not display.