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Table 1 Description of the datasets included in the current version of CellMiner. More will be added on a continuing basis.

From: CellMiner: a relational database and query tool for the NCI-60 cancer cell lines

S.no Data set Description Reference
DNA    
1 aCGH DNA copy number changes from bacterial artificial chromosome array Bussey et al., 2006[5]
2 Mutation DNA sequencing data on mutations on 24 human cancer genes Ikediobi et al, 2006[20]
3 Methylation of E-cadherin promoter PCR amplification and sequencing of sodium bisulfite modified DNA Reinhold et al, 2007[22]
RNA    
4 cDNA cDNA clone microarray with 9,607 features Scherf et al, 2000; Shankavaram et al., 2007[6, 12]
5 HU6800 Affymetrix 6,800-feature microarray Shankavaram et al., 2007[6]
6 HGU95 Affymetrix 64,000-feature microarray Shankavaram et al., 2007[6]
7 HGU133 Affymetrix 44,000-feature microarray Shankavaram et al., 2007[6]
8 ABC transporter RT-PCR data on 47 ABC transporters Szakacs, et al., 2004[15]
9 Ion transporter 632-feature 70-mer oligo microarray Huang et al., 2004[23]
10 NCI-60 radiation Microarray with 612 ESTs plus another set of 616 ESTs chosen on the basis of their known roles in cancer lymphoid biology Amundson et al., 2008[24]
11 microRNA 627 human microRNA probes, including 321 mature microRNAs, as well as probes for most of their precursors. Blower et al., 2007[25]
Protein    
12 RPLA Reverse phase antibody lysate array with detection using 156 monoclonal antibodies Nishizuka et al, 2003; Shankavaram et al., 2007[6, 14]
Drug    
13 A118 The "mechanism of action" set with 6 compound classes. The list of compounds was assembled for an earlier study as training set for neural network analysis of drug mechanism of action. Weinstein et al., 1992 [18]
14 A1429 Combination of A118 and A1400 selected from > 70,000 tested, publicly available compounds by applying a series of filters (see text for description) Scherf et al., 2000; Szakacs et al., 2004[12, 15]
15 A4463 Selected compounds tested in the NCI DTP's sulforhodamine B assay two or more times and for which structure records are available. Blower et al., 2002[19]