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Data sets and Databases
Dana Farber ICBP Data:
Contact: Michael Reich, Broad (Dana Farber ICBP)
Broad Cancer Program publications and datasets: http://www.broad.mit.edu/cgi-bin/cancer/publications/pub_menu.cgi
This page contains publications and datasets published by members of the Broad Institute's Cancer Program
EpigeneDB
Contact: Tim Huang, OSU (OSU ICBP)
http://cancer.informatics.indiana.edu/Nephew_lab/EpigeneDB
EpigeneDB is a collection of gene methylation information from our in-house experiments and as well as from literature searches. Users can browse the database in two ways: “by tumor” or “by gene”.
OMGProm - Database of Orthologous Mammalian Gene Promoters
Contact: Tim Huang, OSU (OSU ICBP)
http://bioinformatics.med.ohio-state.edu/OMGProm
OMGProm, a database of Orthologous Mammalian Gene Promoters, is currently composed of human-mouse orthologous gene promoters with corresponding downloadable sequences, alignments (ClustAlW & Blastz) and links to helpful resources.
KbTSMAD - Knowledgebase of TGF-ß/SMAD Signaling Pathway
Contact: Tim Huang, OSU (OSU ICBP)
http://bioinformatics.med.ohio-state.edu/KbTSMAD
KbTSMAD is an information resource exclusively focused on addressing the need for a better understanding of the TGF-ß/SMAD regulatory mechanism. This database currently contains information about the TGF-ß/SMAD signaling pathway and its target gene promoters and a map of experimentally known binding sites of SMADs and transcription factors involved in their regulation. A graphical platform, which contains a representative overview of the signaling pathway, is also linked to functional information and regulatory preferences.
ERTargetDb - Integral Information Resource of Transcription Regulation of Estrogen Receptor Target Genes
Contact: Tim Huang, OSU (OSU ICBP)
http://bioinformatics.med.ohio-state.edu/ERTargetDB
ERTargetDb integrates information from the ongoing Chip-on-chip experiments in our laboratory and patterns across the target gene promoters promoter sequence conservation from the OMGProm database. We will add methylation and acetylation in the future versions of the database.
DICBP Rb-E2F DATABASE
http://icbp.genome.duke.edu/database.html
In addition to database and visualization facilities, this provides a rich resource of data on the Rb-E2F pathway. The data arises from multiple forms of genomic data, model/analysis summaries, and other information relevant to the integrated understanding of the Rb-E2F pathway arising from the program. At present, the database contains human gene interaction data for protein-DNA interactions and protein-protein interactions. The data sources include (from many disparate sources): microarray induction data, transcription factor regulation data, and protein interaction data. Pathways are generated by applying various database rules, and visualized in Cytoscape.
Oncogene signature expression data
http://data.cgt.duke.edu/oncogene.php
Gene expression data and oncogene pathway signatures from the Bild et at (2005) Nature paper (see Papers link)
Contact: Michael Reich, Broad (Dana Farber ICBP)
Broad Cancer Program publications and datasets: http://www.broad.mit.edu/cgi-bin/cancer/publications/pub_menu.cgi
This page contains publications and datasets published by members of the Broad Institute's Cancer Program
EpigeneDB
Contact: Tim Huang, OSU (OSU ICBP)
http://cancer.informatics.indiana.edu/Nephew_lab/EpigeneDB
EpigeneDB is a collection of gene methylation information from our in-house experiments and as well as from literature searches. Users can browse the database in two ways: “by tumor” or “by gene”.
OMGProm - Database of Orthologous Mammalian Gene Promoters
Contact: Tim Huang, OSU (OSU ICBP)
http://bioinformatics.med.ohio-state.edu/OMGProm
OMGProm, a database of Orthologous Mammalian Gene Promoters, is currently composed of human-mouse orthologous gene promoters with corresponding downloadable sequences, alignments (ClustAlW & Blastz) and links to helpful resources.
KbTSMAD - Knowledgebase of TGF-ß/SMAD Signaling Pathway
Contact: Tim Huang, OSU (OSU ICBP)
http://bioinformatics.med.ohio-state.edu/KbTSMAD
KbTSMAD is an information resource exclusively focused on addressing the need for a better understanding of the TGF-ß/SMAD regulatory mechanism. This database currently contains information about the TGF-ß/SMAD signaling pathway and its target gene promoters and a map of experimentally known binding sites of SMADs and transcription factors involved in their regulation. A graphical platform, which contains a representative overview of the signaling pathway, is also linked to functional information and regulatory preferences.
ERTargetDb - Integral Information Resource of Transcription Regulation of Estrogen Receptor Target Genes
Contact: Tim Huang, OSU (OSU ICBP)
http://bioinformatics.med.ohio-state.edu/ERTargetDB
ERTargetDb integrates information from the ongoing Chip-on-chip experiments in our laboratory and patterns across the target gene promoters promoter sequence conservation from the OMGProm database. We will add methylation and acetylation in the future versions of the database.
DICBP Rb-E2F DATABASE
http://icbp.genome.duke.edu/database.html
In addition to database and visualization facilities, this provides a rich resource of data on the Rb-E2F pathway. The data arises from multiple forms of genomic data, model/analysis summaries, and other information relevant to the integrated understanding of the Rb-E2F pathway arising from the program. At present, the database contains human gene interaction data for protein-DNA interactions and protein-protein interactions. The data sources include (from many disparate sources): microarray induction data, transcription factor regulation data, and protein interaction data. Pathways are generated by applying various database rules, and visualized in Cytoscape.
Oncogene signature expression data
http://data.cgt.duke.edu/oncogene.php
Gene expression data and oncogene pathway signatures from the Bild et at (2005) Nature paper (see Papers link)
last modified
2007-02-15 13:09
