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Today…

Developed at the Broad Institute of MIT and Harvard Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, and Mesirov JP. GenePattern 2.0. Nature Genetics 38 no. 5 (2006): pp500-501 GenePattern is supported by funding from the NIH. Today…. Introduction to GenePattern Why What How Demonstration

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Today…

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  1. Developed at the Broad Institute of MIT and HarvardReich M, Liefeld T, Gould J, Lerner J, Tamayo P, and Mesirov JP. GenePattern 2.0. Nature Genetics 38 no. 5 (2006): pp500-501GenePattern is supported by funding from the NIH

  2. Today… • Introduction to GenePattern • Why • What • How • Demonstration • Summary

  3. Challenges • Modern research methods follow a more integrative approach • Tools are not available to biomedical researchers • Tools are difficult to use • Results difficult to interpret correctly

  4. Purpose • Create tools that are easily accessible to biomedical researchers • Allows for a combination of multiple data sources and methods • Allows for “reproducible research”

  5. GenePattern • Offers a repository of analytic and visualization tools: Modules • Easy creation of complex methods from these tools: Pipelines • The rapid development and dissemination of new methods: Programming Environment

  6. 1. Modules • Point and click • ~ 60 analysis modules (handout) • Documentation • Designed for Affymetrix data • 14 different file extensions

  7. 2. Pipelines • Golub et al illustrates need • Records the methods, parameters and data to ensure reproducibility • Allows methods to be “chained” • Published or create new • Easily shared • Assigns version numbers

  8. 3. Programming environment • Libraries allow transparent access to GenePattern modules from R, Matlab and Java • Language independent mechanism to add new tools to the module repository • Tools can be your own or public (e.g. from Bioconductor)

  9. Functional Architecture Taken from Reich et al Nature Genetics 2006

  10. Components • The GenePattern server • The Java Client • The Web Client

  11. Software Architecture Reich et al Nature Genetics 2006

  12. GenePattern • Current version • Release: 2.0.1, Release date 3/2/2006 • OS compatibility: • Windows: XP, 2000, 2003 • Mac: OS X 1.3.9 or later • Unix: Linux, Solaris, Tru64 • Hardware requirements: • 256MB RAM • 500MB disk space

  13. Demonstration http://www.broad.mit.edu/cancer/software/genepattern/

  14. Gene Expression Analysis • Four broad categories • Differential analysis/Marker selection • Prediction • Class discovery • Pathway analysis • Data Formats • Annotations

  15. Proteomics • SELDI, MALDI and LC-MS in mzXML format • Quality assessment • Peak detection • Spectra comparison • Proteomic analysis pipeline • Data conversion

  16. SNP analysis • In alpha testing • Uses high-density SNP microarray data • Copy number alterations • Loss of heterozygosity (LOH) detection

  17. Data preprocessing and conversion • Importing, exporting and file conversion • Normalization, filtering and imputing • ID conversion and annotation • Row and column extraction, transpose, reorder and split data

  18. Comparison of Selected Microarray Analysis Software Platforms Reich et al Nature Genetics 2006

  19. Summary • Has a few minor problems • Is it something MIBLab can use? • Who is user? • What is it missing? Should be easily added

  20. Sources Gould J, Getz G, Monti S, Reich M, Mesirov JP. Comparative Gene Marker Selection suite. Bioinformatics. 2006 May 18; Liefeld T, Reich M, Gould J, Zhang P, Tamayo P, Mesirov JP. GeneCruiser: a web service for the annotation of microarray data. Bioinformatics. 2005 Sep 15;21(18):3681-2. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP. GenePattern 2.0. Nature Genetics 2006 May;38(5):500-1.

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