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

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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
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Today

• Introduction to GenePattern
• Why
• What
• How
• Demonstration
• Summary

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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

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Purpose

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

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GenePattern

1. Offers a repository of analytic and visualization
   tools Modules
2. Easy creation of complex methods from these
   tools Pipelines
3. The rapid development and dissemination of new
   methods Programming Environment

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1. Modules

• Point and click
• 60 analysis modules (handout)
• Documentation
• Designed for Affymetrix data
• 14 different file extensions

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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

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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)

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Functional Architecture
Taken from Reich et al Nature Genetics 2006
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Components

1. The GenePattern server
2. The Java Client
3. The Web Client

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Software Architecture
Reich et al Nature Genetics 2006
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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

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Demonstration
http//www.broad.mit.edu/cancer/software/genepatte
rn/
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Gene Expression Analysis

• Four broad categories
• Differential analysis/Marker selection
• Prediction
• Class discovery
• Pathway analysis
• Data Formats
• Annotations

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Proteomics

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

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SNP analysis

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

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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

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

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

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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 1521(18)3681-2.
• Reich M, Liefeld T, Gould J, Lerner J, Tamayo P,
  Mesirov JP. GenePattern 2.0. Nature Genetics
  2006 May38(5)500-1.