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Bioinformatic Tools

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CellMiner

CellMinerCDB

CIMminer

GoMiner

HT-GoMiner

MatchMiner

SpliceCenter

SpliceMiner


CellMiner A database and query tool designed for the cancer research community to facilitate integration of the molecular datasets generated by the Genomic and Pharmacology Facility and its collaborators on the NCI-60 (Reinhold, Cancer Res, 2012). The datasets accessible through CellMiner are:
  • DNA fingerprinting of the NCI-60 cell line panel (Lorenzi et al, 2009)
  • DNA: aCGH Agilent 44K
  • DNA: Affymetrix 500K SNP
  • DNA: Combined aCGH
  • DNA: Exome sequencing
  • DNA: Illumina 450K methylation
  • DNA: Illumina 1M SNP Beadchip array
  • DNA: Roche NimbleGen 385K aCGH
  • DNA: Bisulfite sequencing of E-cadherin promoter for DNA methylation
  • RNA: 5 Platform gene transcript summary containing quality control values
  • RNA: RT-PCR analysis for 48 ABC transporters
  • RNA: Affymetrix HG-U133 44K probeset microarray
  • RNA: Affymetrix HG-U133 Plus 2.0
  • RNA: Affymetrix HG-U95 65K probeset microarray
  • RNA: Affymetrix HuEx 1.0 probeset microarray
  • RNA: Agilent mRNA
  • RNA: Agilent Human miRNA (V2)
  • RNA: microRNA expression using the OSU-CCC-hsa-miRNA-chip-V3 array
  • RNA: Ohio State Univ. membrane transporter and channel gene microarray
  • Protein: Reverse-phase Lysate array
  • DTP Drug activities measured for 50% growth inhibition. This includes more than 20,000 compounds, with 187 FDA-approved, 75 clinical trail and 453 know mechanism-of-actions drugs.
New toolCellMinerCDB CellMiner Cross Database (CDB) is the first web application to allow translational researchers to conduct analyses across all major cancer cell line pharmacogenomic data sources from NCI-DTP NCI-60, Sanger GDSC, and Broad CCLE/CTRP. It provides matched molecular and drug activity profiling data. This data may be used to 1) assess molecular and drug data reproducibility, 2) determine repositioning opportunities for FDA-approved compounds, 3) identify potential drug response and gene regulatory determinants, and 4) identify and validate novel genes associated with phenotypic processes. This data is an important precision medicine resource.
CIMminer Generates color-coded Clustered Image Maps (CIMs) ("heat maps") to represent high-dimensional data sets such as gene expression profiles. We introduced CIMs in the mid-1990’s for data on drug activity, target expression, gene expression, and proteomic profiles. Clustering of the axes brings like together with like to create patterns of color. (Weinstein, et al., Science 1997; 275:343-349)
GoMiner Addresses the question, "Now that I’ve done the gene expression experiment and identified a set of ‘interesting’ genes, what do those genes mean biologically?" GoMiner batch-processes and organizes lists of thousands or tens of thousands of genes and provides two fluent, robust visualizations of the genes in the framework of the Gene Ontology hierarchy. (Zeeberg, et al., Genome Biology 2003; 4:R28)
High-Throughput GoMiner High-Throughput GoMiner has the capabilities of GoMiner and a number of others. It automates the analysis of multiple microarrays and integrates results across all of the microarrays, and will be useful in a wide range of applications, including the study of time-courses, evaluation of multiple drug treatments, comparison of multiple gene knock-outs or knock-downs, and screening of large numbers of chemical derivatives generated from a promising lead compound. (Zeeberg and Qin, et al., BMC Bioinformatics. 2005 Jul 5;6(1):168.)
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., BMC Bioinformatics. 2008 9:13)
SpliceMiner Provides an intuitive non-redundant display of a gene's splice variants and may be searched by gene symbol, chromosomal position, or probe sequence. SpliceMiner is particularly useful in determining which splice variants are targeted (or missed) by a microarray probe, PCR primer, or siRNA. A high-throughput interface is available for batch processing of large numbers of queries. (Kahn AB, et al., BMC Bioinformatics. 2007 Mar 5;8(1):75)
MatchMiner Translates among gene identifier types for lists of hundreds or thousands of genes. Included: GenBank accession numbers, IMAGE clone IDs, common gene names, HUGO names, gene symbols, UniGene clusters, FISH-mapped BAC clones, Affymetrix identifiers, and chromosome locations. MatchMiner can also find the intersection of two lists of genes specified by different identifiers. (Bussey, et al., Genome Biology 2003; 4:R27)
AbMiner A relational database of information on antibodies that we have screened specificity against the NCI-60 cancer cell lines. The database includes results of screenings by western blot, practical information for purchase, identifiers such as UniGene cluster and gene name for each antibody, and out-links to major public bioinformatics resources. (Major, et al., BMC Bioinformatics 2006, 7:192)
Retired Tools - no longer being maintained by the Genomic and Pharmacology Facility
AffyProbeMiner AffyProbeMiner is to re-define chip definition files (CDFs) for Affymetrix chips taking into account the most recent genomic sequence information. It re-groups probes in Affymetrix chips into probe sets according to a list of non-redundant verified complete coding sequences available in GenBank and RefSeq. Pre-computed CDFs for several chips are available for download. (Liu HF, et al., Bioinformatics. 2007 Sep 15;23(18):2385-90.)

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