GenMAPP and MAPPFinder for Systems Biology Education Kam Dahlquist Vassar College June 12-20, 2004 BioQUEST Summer Workshop Beloit College.

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Presentation transcript:

GenMAPP and MAPPFinder for Systems Biology Education Kam Dahlquist Vassar College June 12-20, 2004 BioQUEST Summer Workshop Beloit College

Merged, false color image Green = Cy3 Red = Cy5 Output is ratio of fluoresence intensities Printed Microarray Scott Freeman, Biological Science (2002) Fig a

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 Institutes Bruce Conklin Scott Doniger Lynn Ferrante Kristina Hanspers Steven Lawlor Alex Pico Nathan Salomonis Karen Vranizan Alex Zambon Vassar College Meredith Braymer ‘04 Jessica Heckman ‘05 David Koren ’06 Christen Vogel ’04