Systems Biology: The Annual BioQUEST Summer Workshop 2004

Workshop Announcement

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GenMAPP and MAPPFinder for Systems Biology Education

Authors Audiences Overview Materials Resources Future Directions

Authors

Kam Dahlquist
Loyola Marymount University

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Possible Audiences:

Introductory Biology
Genetics
Biochemistry
Molecular Biology
Cell Biology
Bioinformatics

Brief Overview

GenMAPP is a computer program designed for viewing and analyzing gene expression data on MAPPs representing biological pathways or any other functional grouping of genes.

MAPPFinder is an accessory program that works with GenMAPP and the annotations from the Gene Ontology (GO) Consortium to identify global biological trends in gene expression data.

The GenMAPP and MAPPFinder system provides a framework for learning about the properties of biochemical and gene regulatory pathways. Students can research a pathway in conjunction with a course topic and then draw it out with the GenMAPP graphics tools. Students can then color-code the pathway with publicly available microarray data, connecting them to cutting-edge research. The pathways the students draw can be submitted to the public pathway repository at www.GenMAPP.org, their work making a contribution to practicing scientists. In summary, the systems level approach provided by GenMAPP moves seamlessly from class projects to independent research and will allow students to make a contribution to the scientific community.

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Project Materials

GenMAPP and MAPPFinder are free, Windows-only applications that must be installed on a local computer. The installer for version 2 of both programs can be downloaded from www.GenMAPP.org. During the installation you will be prompted to download Gene Databases, MAPPs, and Expression Datasets. Download the materials for the species in which you are interested.

The exercises described in this project used the human prostate cancer dataset (Hs_ED_ProstateCancer_20040209.gex) and the yeast metabolic timecourse dataset (Sc_ED_MetabTimeCourse-DeRisi-sci_20040127.gex) available from GenMAPP.org. The PowerPoint presentation from the BioQUEST workshop and Word documents describing the exercises can be found below.

Resources and References

GenMAPP and MAPPFinder online tutorial

Dahlquist et al. (2000) Nature Genetics 31:19-20. The manuscript describing GenMAPP 1.0.

Doniger et al. (2002) Genome Biology 4:R7. The manuscript describing MAPPFinder 1.0 using an Expression Dataset comparing a 12.5 day embryonic mouse heart to an adult mouse heart.

LaTulippe et al. (2002) Cancer Research 62:4429. The manuscript associated with the human prostate cancer dataset. The manuscript only describes the primary vs. metastatic tumor comparison. Data for two other comparisons, primary vs. treated tumor and primary vs. androgen independent tumor are included in the Expression Dataset.

DeRisi et al. (1997) Science 278:680. The manuscript associated with the yeast metabolic timecourse dataset.

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Future Directions

Student work on GenMAPP MAPPs, Expression Datasets, and Gene Databases will be posted on the web. I hope to incorporate the current exercises into larger systems biology modules involving cancer biology and yeast functional genomics. I will also be creating an exercise where advanced students can construct new Gene Databases for use with GenMAPP and MAPPFinder.

Attachments

- MAPPFinder-GenMAPPAssignment_yeast.doc
- DeRisi_Science_97.pdf
- LaTulippe_CancerRes_02.pdf
- Doniger_GenomeBiology_03.pdf
- Dahlquist_NatGenet_02.pdf
- Dahlquist_BioQUEST_6-12-04.ppt
- MAPPFinderAssignment_prostatecancer.doc

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