| Mission and Central activities: |
| The GBG's mission is to manage and assess molecular interaction data obtained through multiple platforms,
increase the understanding of the effect of those interactions on the chemosensitivity of cancer, and create tools
that will facilitate that process. Translation of that information will be directed towards the recognition of
diagnostic and therapeutic cancer biomarkers, and directed cancer therapy. |
| Freely available for public use are our professional grade Miner Suite bioinformatics software package, as well as
our characterization and annalysis of the NCI-60 cancer cell lines, the DNA, RNA, protein, epigenetic and pharmacological
levels (accessible through CellMiner).
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| The Miner Suite of bioinformatic software packages and data analysis. |
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SpliceCenter: A suite of very user-friendly tools
designed for use by every bench biologist who needs to check for the impact of gene splice variation on common molecular biology technologies
including RT-PCR, RNAi, expression microarrays, and peptide-based assays (Ryan et al., 2008). 
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SpliceMiner: A web application for mapping microarrray probes to
transcripts in an exon-specific manner (Kahn et al, 2007).
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GoMiner: A tool that leverages the Gene Ontology for biological interpretation of microarrays
data (Zeeberg et al, 2003).
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High-Throughput GoMiner: A tool for batch processing of multiple microarrays and
integrated CIMs of the GoMiner results (Zeeberg et al, 2005).
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CIMminer: A tool that produces Clustered Image Maps (CIMs) (i.e., clustered heat maps)
(Weinstein et al, 1997).
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LeFEminer: A statistical/machine learning algorithm for interpreting gene microarray datasets using independently
determined gene categories such as those defined by GO, KEGG and MSigDB (Eichler et al, 2007).
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AffyProbeMiner: A bioinformaticists web resource for computing and retrieving accurately
redefined Affymetrix probe sets (Liu et al, 2007).
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MIMminer: A repository of the electronically navigatable Kohn Molecular Interaction Maps
(Kohn and Aladjem, 2006).
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MatchMiner: A tool for batch-translation among many types of gene and protein identifiers
(Bussey et al, 2003).
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SmudgeMiner: A tool for highlighting regional biases and other artifacts on Affymetrix and other
microarrays to enable quality assessment (Reimers and Weinstein, 2005).
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| Molecular databases for integromic research on the NCI-60 cancer cells |
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- CellMiner: A database and query tool
designed for the cancer research community to facilitate integration of the molecular datasets generated by the GBG
and its collaborators on the NCI-60. (Shankavaram et al., 2009)
The datasets accessible through CellMiner are:
- DNA fingerprinting of the NCI-60 cell line panel (Lorenzi et al, 2009)
- DNA: aCGH Agilent 44K
- DNA: Bisulfite sequencing of E-cadherin promoter for DNA methylation
(Reinhold et al., 2007)
- DNA: Sequence mutation analysis of 24 known cancer genes
(Ikediobi et al., 2006)
- RNA: Agilent mRNA
(Liu et al., 2010)
- RNA: Agilent Human miRNA (V2)
(Liu et al., 2010)
- RNA: Ionizing Radiation 6727 probe, 2-color microarray
(Amundson et al., 2008)
- RNA: microRNA expression using the OSU-CCC-hsa-miRNA-chip-V3 array
(Blower et al., 2007)
- RNA: Affymetrix HG-U133 44K probeset microarray
(Shankavaram et al., 2007)
- RNA: Affymetrix HG-U95 65K probeset microarray
(Shankavaram et al., 2007)
- RNA: RT-PCR analysis for 48 ABC transporters
(Szakács et al., 2004)
- RNA: Ohio State Univ. membrane transporter and channel gene microarray
(Huang et al., 2004)
- RNA: cDNA 2-color array using the Incyte, Inc. 9700 clone microarray
(Shankavaram et al., 2007; Scherf et al., 2000; Ross et al., 2000)
- Protein: Reverse-phase Lysate array
(Nishizuka et al., 2003; Shankavaram et al., 2007)
- Drug: A118 - Activities of 118 drugs with known 2D structure, mechanism of action and tested at least 4 times
(Bussey et al., 2006)
- Drug: A1429 - Activities of 1429 drugs with known 2D structure and tested at least 4 times
(Annereau et al., 2004)
- Drug: A4463 - Activities of 4463 drugs with known 2D structure and tested at least 2 times
(Blower et al., 2002)
- DNA: Spectral karyotyping of chromosomal aberrations
(Roschke et al., 2003)
available at NCBI SKY/M-FISH and CGH Database
or SKYGRAMS at NCI DTP
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