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

15. Merged, false color image Green = Cy3 Red = Cy5 Output is ratio of fluoresence intensities Printed Microarray Scott Freeman, Biological Science (2002) Fig. 16.10a

16. Redfern et al. (2000) PNAS 97:4826

21. Dahlquist et al. (2000) Nature Genetics 31:19

23. GenMAPP Demo

25. Doniger et al. (2002) Genome Biology 4:R7

28. 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.

29. MAPPFinder Demo

34. 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

35. Acknowledgments Gladstone Institutes Bruce Conklin Scott Doniger Lynn Ferrante Kristina Hanspers Steven Lawlor Alex Pico Nathan Salomonis Karen Vranizan Alex Zambon www.GenMAPP.org genmapp@gladstone.ucsf.edu Vassar College Meredith Braymer ‘04 Jessica Heckman ‘05 David Koren ’06 Christen Vogel ’04 kadahlquist@vassar.edu