genmapp and mappfinder for systems biology education kam dahlquist vassar college june 12-20, 2004...
TRANSCRIPT
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
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.
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
Vassar CollegeMeredith Braymer ‘04Jessica Heckman ‘05David Koren ’06Christen Vogel ’04