A Perspective article in the March 28, 2008 issue of Science (A Postgenomic Visual Icon) on clustered heat maps and visualization of massive data sets in postgenomic biology (Weinstein, JN., 2008). Also see our original article in Science on clustered heat maps and "pre-postgenomic" biology (Weinstein, et al., 1997).

   Updated version of CIMminer, a tool for creating clustered heat maps.

  The LeFE algorithm: embracing the complexity of gene expression in the interpretation of microarray data. Eichler, et al.

   CellMiner: A database and query tool coordinated with the SMP series to facilitate integration and fusion of the various molecular datasets generated by the GBG and its many collaborators. Designed for the cancer research community, the goal is to provide a platform for both system wide elucidation of molecular systems and aid in pharmacogenomic research.

The Genomics & Bioinformatics Group (GBG) web site offers useful bioinformatic program packages, microarray data analysis information, and molecular databases for genomic and proteomic research.

Available bioinformatic resources from the GBG (The Miner Suite) include:

• CIMminer: Produces Clustered Image Maps (CIMs) (i.e., clustered heat maps).
• LeFEminer: A tool for interpreting gene microarray datasets using independently determined gene categories such as those defined by GO, KEGG and MSigDB.  
• AffyProbeMiner: A web resource for computing or retrieving accurately redefined Affymetrix probe sets. 
• SpliceMiner: Web application for mapping microarrray probes to splice variants. 
• CellMiner: A database and query tools for molecular profile information on the NCI 60 human cancer cell lines and the DU145/RC0.1 prostate cancer cell line pair. 
• AbMiner: A database resource on available monoclonal antibodies.
• MatchMiner: Batch-translates among many types of gene and protein identifiers.
• GoMiner: Leverages the Gene Ontology for biological interpretation of microarrays data, etc.
• High-Throughput GoMiner: Batch processing of multiple microarrays and integrated CIMs of the results.
• SmudgeMiner: Highlights regional biases and other artifacts on Affymetrix and other microarrays to enable quality assessment.
• MedMiner: Searches and organizes the PubMed literature on genes and drugs.
• MIMminer: Electronically navigates Kohn Molecular Interaction Maps.
• Also: An (opinionated) guide to microarray data analysis.

Available molecular databases on the NCI-60 cancer cells include:

• cDNA microarray gene expression data and correlative drug activity data.
• Affymetrix microarray gene expression data.
• ABC transporter real-time RT-PCR gene expression data.

Central activities of the Genomics & Bioinformatics Group:

Experimental: Characterization of cancer cells at the DNA, mRNA, protein, functional, and pharmacological levels, with focus on discovery of new biomarkers and new treatments for cancer.

Bioinformatic/Biostatistical: Analysis and integration of large-scale databases on diagnostic and therapeutic cancer biomarkers and candidate agents for cancer therapy. This integromic enterprise represents bottom-up systems biology. One product is the Miner Suite of professional grade bioinformatics software freely available for public use.