CellMiner™ is a web application that facilitates systems biology through the retrieval and integration of the various molecular data sets generated by the Genomics & Bioinformatics Group, LMP, CCR, NCI and its many collaborators. Subsequent builds will include additional molecular data sets and integrative capabilities. CellMiner was developed as a companion for the Spotlight on Molecular Profiling series, which we launched with 3 articles in Molecular Cancer Therapeutics in November 2006.

• 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.

CellMiner Data Sets

• DNA fingerprinting of the NCI-60 cell line panel (Lorenzi et al, 2009) To download the DNA fingerprinting data for the NCI-60 click here or to learn how to compare your DNA fingerprints to those of the NCI-60, click here. This infomation is also available in CellMiner under Cell Line Metadata.
  
• DNA: Roche NimbleGen 385K aCGH (Reinhold et al, 2010)
• DNA: aCGH Agilent 44K
• DNA: Bisulfite sequencing of E-cadherin promoter for DNA methylation (Reinhold et al., 2007)
• DNA: Sequence mutation analysis of 24 known cancer genes (Ikediobi et al., 2006)



• RNA: Affymetrix HuEx 1.0 (Reinhold et al., 2010)
• RNA: Agilent mRNA (Liu et al., 2010)
• RNA: Agilent Human miRNA (V2) (Liu et al., 2010)
• RNA: Affymetrix HG-U133 Plus 2.0 (Reinhold et al, 2009) (Pfister et al, 2009)
• RNA: microRNA expression using the OSU-CCC-hsa-miRNA-chip-V3 array (Blower et al., 2007)
• RNA: Affymetrix HG-U133 44K probeset microarray (Shankavaram et al., 2007)
• RNA: Affymetrix HG-U95 65K probeset microarray (Shankavaram et al., 2007)
• RNA: RT-PCR analysis for 48 ABC transporters (Szakács et al., 2004)
• RNA: Ohio State Univ. membrane transporter and channel gene microarray (Huang et al., 2004)



• Protein: Reverse-phase Lysate array (Nishizuka et al., 2003; Shankavaram et al., 2007)



• Drug: A118 - Activities of 118 drugs with known 2D structure, mechanism of action and tested at least 4 times (Bussey et al., 2006)
• Drug: A1429 - Activities of 1429 drugs with known 2D structure and tested at least 4 times (Annereau et al., 2004)
• Drug: A4463 - Activities of 4463 drugs with known 2D structure and tested at least 2 times (Blower et al., 2002)

How to find the information you need in CellMiner

• For DNA, RNA or Protein data use the:
• Data Set Metadata tab to get background information about each data set.
• Download Genomic Data Sets tab to download the entire data set, in either raw or normalized versions.
• Query Genomic Data Sets tab to query the normalized data sets for information. You can search the data using single identifiers, or a list of identifiers, customize your data annotation, and select your output data format.
• For drug data use the:
• Data Set Metadata tab to get details about the different drug datasets.
• Query Drug Data Sets tab to search the 50% growth inhibition data for the NCI-60, for 3 variably curated DTP drug sub-sets. Multiple types of background information are available, including chemical name, molecular formula, and Simplified Molecular Input Line Entry Specification (SMILES). You can download the entire data set or query for a particular drug by NSC number or chemical formula or a group of drugs by partial name match like 'cyclin'.
• For Sequence Mutation with analysis for 24 genes use the:
• Mutation Data tab to get a list of mutations found in 24 known, important human cancer genes.
• Query Genomic Data Sets tab to query for specified genes. Be sure to check the include mutation data box.
• For cell line and citation information use the:
• Cell Line Metadata tab to view metadata on the NCI-60 panel and DU145/RC0.1 pair. Included are tissue type, patient demographics, prior treatment, histology, source, ploidy, p53 status, DNA fingerprint data, etc. Queries can be limited to particular tissues of origin
• Citing CellMiner tab to see a list of references for citing CellMiner and their associated data sets.

Links

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

For additional drug, dataset and molecular target data see the NCI Developmental Therapeutics Program site.

CellMiner Development Team

Margot Sunshine, Uma Shankavaram, William Reinhold, prior contributors