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

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]