Developed at the Broad Institute of MIT and Harvard Reich M, Liefeld T, Gould J, Lerner J, Tamayo P,...
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Transcript of Developed at the Broad Institute of MIT and Harvard Reich M, Liefeld T, Gould J, Lerner J, Tamayo P,...
![Page 1: 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.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649f315503460f94c4be0a/html5/thumbnails/1.jpg)
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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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/genepattern/
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Gene Expression Analysis
• Four broad categories1. Differential analysis/Marker selection
2. Prediction
3. Class discovery
4. 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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SourcesGould 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.