Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract CellMiner is a database and query tool coordinated with the Spotlight on Molecular Profiling (SMP) series to facilitate integration and fusion of the various molecular datasets generated by the Genomics & Bioinformatics Group (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.

CellMiner provides data sets and query tools for the following:

1) 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.

2) 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.

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.

CellMiner features/capabilities include:

Cell Line Metadata --

This feature 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 --

This feature provides background information about each data set, such as Name, Platform Information, Principal Collaborators and Data Description.

Download Raw Data Set --

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 (3) query options:

1) Query by single gene identifier (HUGO symbol, Entrez Gene ID, Gene Name, mRNA RefSeq, protein RefSeq).

2) Query by chromosome identifier (chromosome number, CytoBand, or transcript range).

3) Query by platform specific identifier (Affy id).

Data Intersection --

This feature allows you to select the data to be included in your output and download data on genes common to two (2) or more platforms.

Query Drug Data Sets --

Search 50% growth inhibition data for the NCI-60, for 3 variably curated Development Therapeutics Program (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 the NCI-60 DNA is being sequencing for mutations in known human cancer genes. Cells were supplied by the NCI/NIH Developmental Therapeutics Program.

The coding exons and immediate flanking intron sequences of selected genes from the Cancer Gene Census have been PCR-amplified and sequenced.

The results have been entered in the Catalogue of Somatic Mutations in Cancer (COSMIC) database and web site.

Further genes are currently being sequenced to expand the mutation data on the NCI-60. DNA sequence mutations were confirmed in at least two (2) independent experiments.

System Requirements

Contact manufacturer.


CellMiner is a development of the

Manufacturer Web Site CellMiner

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G6G Abstract Number 20262

G6G Manufacturer Number 101841