1 / 35

Merged, false color image Green = Cy3 Red = Cy5 Output is ratio of fluoresence intensities

GenMAPP and MAPPFinder for Systems Biology Education Kam Dahlquist Vassar College June 12-20, 2004 BioQUEST Summer Workshop Beloit College. Printed Microarray. Merged, false color image Green = Cy3 Red = Cy5 Output is ratio of fluoresence intensities.

gunda
Download Presentation

Merged, false color image Green = Cy3 Red = Cy5 Output is ratio of fluoresence intensities

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. GenMAPP and MAPPFinder for Systems Biology EducationKam DahlquistVassar CollegeJune 12-20, 2004BioQUEST Summer WorkshopBeloit College

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

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

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

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

  6. GenMAPP Demo

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

  8. 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.

  9. MAPPFinder Demo

  10. 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

  11. 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

More Related