The use of genome-wide expression studies is revolutionizing our approach to understanding normal cellular processes and the mechanisms of disease. Sophisticated computational methods enable the analysis of this data. An important goal is to empower scientists with domain expertise by giving them direct access to these new technologies and techniques for interpretation. However, these computational methods can be difficult to understand and use correctly. They may not easily work together or be reproduced. Over the past 6 years we have been developing advanced mathematical methods and computational algorithms for the analysis of microarray data. We share them with the research community in user-friendly, freely available software packages, GeneCluster and GenePattern. GenePattern was released in March 2004 and represents a major reworking, improvement, and expansion of the GeneCluster application. The power of GenePattern is its accessibility to a broad community of users, the ability to access and interoperate a library of analytic and visualization modules, and the ease with which the environment supports the rapid development and dissemination of new methods. Our goal is to continue to make this software available to and useful for the research community.
Aim 1. Continuing user support for the GenePattern and GeneCluster packages.
Aim 2. Enhancements to GenePattern to better support users and their research.
Aim 3. Continuing software maintenance of the GenePattern and GeneCluster Packages. Our extensive experience in software engineering, significant user base, development of preliminary documentation, and successful workshops for users make us well poised to carry out the aims of this proposal.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM074024-02
Application #
7070627
Study Section
Special Emphasis Panel (ZRG1-BST-D (51))
Program Officer
Remington, Karin A
Project Start
2005-06-01
Project End
2009-05-31
Budget Start
2006-06-01
Budget End
2007-05-31
Support Year
2
Fiscal Year
2006
Total Cost
$461,381
Indirect Cost
Name
Massachusetts Institute of Technology
Department
Type
Organized Research Units
DUNS #
001425594
City
Cambridge
State
MA
Country
United States
Zip Code
02139
Archer, Tenley C; Ehrenberger, Tobias; Mundt, Filip et al. (2018) Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups. Cancer Cell 34:396-410.e8
Kim, Jong Wook; Abudayyeh, Omar O; Yeerna, Huwate et al. (2017) Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States. Cell Syst 5:105-118.e9
Carlin, Daniel; Kosnicki, Kassi; Garamszegi, Sara et al. (2017) A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Res 6:784
Silterra, Jacob; Gillette, Michael A; Lanaspa, Miguel et al. (2017) Transcriptional Categorization of the Etiology of Pneumonia Syndrome in Pediatric Patients in Malaria-Endemic Areas. J Infect Dis 215:312-320
Viswanathan, Vasanthi S; Ryan, Matthew J; Dhruv, Harshil D et al. (2017) Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway. Nature 547:453-457
Reich, Michael; Tabor, Thorin; Liefeld, Ted et al. (2017) The GenePattern Notebook Environment. Cell Syst 5:149-151.e1
Dhingra, Priyanka; Martinez-Fundichely, Alexander; Berger, Adeline et al. (2017) Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network. Genome Biol 18:141
Boulay, Gaylor; Awad, Mary E; Riggi, Nicolo et al. (2017) OTX2 Activity at Distal Regulatory Elements Shapes the Chromatin Landscape of Group 3 Medulloblastoma. Cancer Discov 7:288-301
Durand, Neva C; Robinson, James T; Shamim, Muhammad S et al. (2016) Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. Cell Syst 3:99-101
Zhu, Xiaodong; Girardo, David; Govek, Eve-Ellen et al. (2016) Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation. Neuron 89:100-12

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