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