Post on 23-Feb-2016
description
GenMAPP and MAPPFinder for Systems Biology Education
Kam DahlquistVassar College
June 12-20, 2004BioQUEST Summer Workshop
Beloit College
Merged, falsecolor image
Green = Cy3
Red = Cy5
Output isratio of fluoresenceintensities
Printed Microarray
Scott Freeman, Biological Science (2002) Fig. 16.10a
Redfern et al. (2000) PNAS 97:4826
Redfern et al. (2000) PNAS 97:4826
Dahlquist et al. (2000) Nature Genetics 31:19
GenMAPP Demo
Doniger et al. (2002) Genome Biology 4:R7
Permute P Value and Adjusted P Value
• To generate a p value from the Z score, MAPPFinder permutes the data 1000 times and calculates new Z scores from each permutation of the data. This distribution of Z scores is used to calculate the permute p value.
• Since thousands of p values are being calculated, there is a multiple testing problem. If a p value cut-off of p<0.05 is chosen, 5% of the p values could be “significant” by chance. MAPPFinder performs the Westfall-Young adjustment on the p values to generate the adjusted p which is very stringent.
MAPPFinder Demo
Hands-on Exercises• Student exercises piloted this year in
introductory biology and intermediate genetics courses
• Intro bio students analyzed a human prostate cancer dataset with MAPPFinder
• Genetics students analyzed a yeast metabolic timecourse dataset with MAPPFinder and drew the adenine biosynthesis pathway with GenMAPP
• A dataset comparing gene expression in the heart of a 12.5 day mouse embryo to an adult heart is also available
Acknowledgments
Gladstone InstitutesBruce ConklinScott DonigerLynn FerranteKristina HanspersSteven LawlorAlex PicoNathan SalomonisKaren VranizanAlex Zambon
www.GenMAPP.orggenmapp@gladstone.ucsf.edu
Vassar CollegeMeredith Braymer ‘04Jessica Heckman ‘05David Koren ’06Christen Vogel ’04
kadahlquist@vassar.edu