CellMiner™ is a web application that provides data sets and query tools for the following:

• The NCI-60, a panel of 60 diverse human cancer cell lines used by the Developmental Therapeutics Program of the U.S. National Cancer Institute to screen >100,000 compounds and natural products since 1990.

• The DU145/RC0.1 prostate cancer cell line pair. RC0.1 is a derivative of DU145 selected for resistance to the Topoisomerase I inhibitor Camptothecin.

We developed CellMiner as a companion for the Spotlight on Molecular Profiling series, which we launched with 3 articles in Molecular Cancer Therapeutics in November 2006.

CellMiner is designed to facilitate integration and fusion of the various molecular data sets generated by the Genomics & Bioinformatics Group, LMP, CCR, NCI and its many collaborators. The application includes metadata on the cells, as well as tools for downloading the data set, querying them, and finding the intersections among them. Subsequent builds will include many additional molecular data sets and integrative tools.

For other bioinformatic tools and database resources from GBG go to the Discover website home page.

New!!!Drug activity data for 50% growth inhibition of the NCI-60 from three subsets of the Developmental Therapeutics Program (DTP) data!

Cell Line Metadata

Provides metadata on the NCI-60 panel and DU145/RC0.1 pair. Included, are tissue type, patient demographics, prior treatment, histology, source, ploidy, p53 status, etc. Queries can be limited to particular tissues of origin.

Data Set Metadata

Provides background information about each data set.

Download Genomic Data Sets

Download raw or normalized data. Selecting "Raw Data" downloads .cel files, pixel intensities, or the like, depending on platform. Selecting "Normalized Data" downloads processed values ready for analysis and/or integration with other data sets.

Query Genomic Data Sets

Search data by single identifier or list of identifiers, and retrieve additional annotation information. There are three query options: Query by single gene identifier (HUGO symbol, Entrez Gene ID, Gene Name, mRNA RefSeq, protein RefSeq). Query by chromosome identifier (chromosome number, CytoBand, or transcript range). Query by platform specific identifier (Affy id).

Data Intersection

Download data on genes common to two or more platforms.

Query Drug Data Sets

Search 50% growth inhibition data for the NCI-60, for 3 variably curated DTP drug sub-sets. Included is the stringently tested 118 set of drugs with known mechanisms of action. Multiple types of drug background information are available, including chemical name, molecular formula, and Simplified Molecular Input Line Entry Specification (SMILES).

Mutation Data

In collaboration with the Wellcome Trust Sanger Institute we are sequencing the NCI-60 for mutations in known, important human cancer genes. (See Ikediobi, et al.)

Credits

A list of the hard working people who made CellMiner possible.

Citing CellMiner

A collection of references for citing CellMiner and also the individual data sets in it.

Links

Also see molecular targets at the NCI Developmental Therapeutics Program site.