NCI Genomics and Pharmacology Facility

Established Technologies

• CellMiner – Comprehensive molecular data on the NCI-60 cancer cell lines, including:
  1. Multiple microarray platforms measuring gene expression
  2. Gene transcript level z score determination from 5 microarray platforms
  3. aCGH DNA copy number
  4. MicroRNA expression and SNP status
  5. Pattern comparison between transcript expression, microRNA expression, and drug activity for any input pattern of interest to the user
  6. Access to exome sequencing for all genes in the NCI-60 cell line
  7. Drug activity z score provides activity levels for 22,257 compounds, including 190 FDA-approved and 365 in clinical trial drugs. These are derived from the Developmental Therapeutics Program (DTP) GI50 experiments (http://dtp.nci.nih.gov/)

CellMiner is available to the public as a Web-based query and analysis tool at http://discover.nci.nih.gov/cellminer.

• CellMinerCDB (cross database) – 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
  4. Identify and validate novel genes associated with phenotypic processes
• This data is an important precision medicine resource.

In addition, the following tools are available via the Discover Web site:

• GOMiner – A tool that leverages the gene ontology for biological interpretation of microarray data
• CIMminer – Create clustered maps (heatmaps) of matrix data (such as gene expression)
• SpliceCenter – A suite of 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.
• MIMminer – A repository of the electronically navigatable Kohn molecular interaction maps
• AbMiner – A tool that allows users to search for appropriate, commercially available antibodies for research purposes, and to match each antibody to its respective genomic identifiers.

Developing Technologies

We are currently developing disease-specific versions of CellMinerCDB to ease and focus studies associated with those diseases.