Gene DNA copy number

This tool provides access to the DNA copy number computed as a combined value from four array-CGH platforms: Agilent 44K, Affymetrix 500K, NimbleGen 385K and Illumina 1M.

The tool provides an Excel spreadsheet for each gene that includes:

  1. the estimated DNA copy number in tabular and graphical forms (see below),
  2. scatter plots of the probes intensities that fall within the gene in addition to 2 million nucleotides flanking region,
  3. the normalized data for those probes that fall within a gene of interest as well as its flanking regions in tabular form.

The data is queryable by gene or chromosomal location using Query Genomic Data under "DNA: Combined aCGH" (http://discover.nci.nih.gov/cellminer/queryLoad.do).
The data may be obtained in toto at Download Data Sets under "DNA: Combined aCGH" (http://discover.nci.nih.gov/cellminer/loadDownload.do).
A brief platform description is available in Data Set Metadata under "DNA: Combined aCGH" (http://discover.nci.nih.gov/cellminer/datasets.do).


Table 1: Estimated DNA copy values
Cell lines Mean intensity Copy
Cell lines ratios number

BR:MCF7 0.15 2.22
BR:MDA_MB_231 -0.24 1.69
BR:HS578T 0.36 2.57
BR:BT_549 -0.03 1.96
BR:T47D 0.11 2.16
CNS:SF_268 -0.03 1.95
CNS:SF_295 0.00 1.99
CNS:SF_539 0.47 2.76
CNS:SNB_19 -0.06 1.92
CNS:SNB_75 0.11 2.16
CNS:U251 -0.07 1.9
CO:COLO205 0.32 2.49
CO:HCC_2998 0.05 2.07
CO:HCT_116 0.03 2.04
CO:HCT_15 0.08 2.11
CO:HT29 0.30 2.47
CO:KM12 0.04 2.06
CO:SW_620 -0.08 1.89
LE:CCRF_CEM 0.14 2.21
LE:HL_60 0.05 2.07
LE:K_562 -0.27 1.65
LE:MOLT_4 0.05 2.07
LE:RPMI_8226 0.10 2.15
LE:SR -0.01 1.99
ME:LOXIMVI -0.03 1.95
ME:MALME_3M 0.12 2.17
ME:M14 0.24 2.36
ME:SK_MEL_2 0.22 2.34
ME:SK_MEL_28 0.37 2.58
ME:SK_MEL_5 0.11 2.15
ME:UACC_257 0.15 2.22
ME:UACC_62 0.52 2.86
ME:MDA_MB_435 0.44 2.70
ME:MDA_N 0.035 2.55
LC:A549 -0.29 1.64
LC:EKVX -0.27 1.66
LC:HOP_62 0.10 2.15
LC:HOP_92 -0.03 1.95
LC:NCI_H226 0.09 2.13
LC:NCI_H23 0.13 2.19
LC:NCI_H322M -0.13 1.83
LC:NCI_H460 -0.12 1.84
LC:NCI_H522 -0.20 1.74
OV:IGROV1 -0.06 1.92
OV:OVCAR_3 0.40 2.64
OV:OVCAR_4 0.34 2.52
OV:OVCAR_5 -0.13 1.82
OV:OVCAR_8 0.29 2.44
OV:SK_OV_3 0.05 2.08
OV:NCI_ADR_RES 0.35 2.55
PR:PC_3 -0.14 1.82
PR:DU_145 -0.19 1.75
RE:786_0 0.16 2.23
RE:A498 -0.03 1.96
RE:ACHN -0.07 1.90
RE:CAKI_1 0.07 2.10
RE:RXF_393 -0.25 1.69
RE:SN12C 0.71 2.26
RE:TK_10 0.19 2.28
RE:UO_31 0.32 2.50

 
 
     

Scatter plot