Five platform transcript compilation and correlation tool
This tool compiles all transcript probe date from five microarray platforms for user specified genes.
These platforms are the Affymetrix Human Genome U95, Human Genome U133, Human Genome U133 Plus 2.0,
GeneChip® Human Exon 1.0 ST Array, and the Agilent Whole Human Genome Oligo Microarray.
The user is allowed to submit a list of up to 150 genes. The tool provides an Excel spreadsheet for each gene.
The tool performs quality control for all probes available for a given gene, gives the intensity values
for those probes that pass the quality control, and provides a single Z score value for each cell line in the NCI-60,
in both tabular and graphical forms. In addition, the user may select to recieve a summary sheet which contains the
Z scores for all the gene in the user's list and an automatic correlation comparison between all possible gene combinations present.
Below is a section of some sample output.
| cell lines |
average Z scores |
|
| BR:MCF7 |
1.31 |
|
| BR:MDA_MB_231 |
-1.01 |
|
| BR:HS578T |
-0.39 |
|
| BR:BT_549 |
0.88 |
|
| BR:T47D |
0.64 |
|
| CNS:SF_268 |
-0.49 |
|
| CNS:SF_295 |
-0.69 |
|
| CNS:SF_539 |
na |
|
| CNS:SNB_19 |
-1.39 |
|
| CNS:SNB_75 |
-0.42 |
|
| CNS:U251 |
-0.96 |
|
| CO:COLO205 |
0.49 |
|
| CO:HCC_2998 |
1.04 |
|
| CO:HCT_116 |
1.23 |
|
| CO:HCT_15 |
1.62 |
|
| CO:HT29 |
1.35 |
|
| CO:KM12 |
0.75 |
|
| CO:SW_620 |
-0.92 |
|
| LE:CCRF_CEM |
0.61 |
|
| LE:HL_60 |
1.28 |
|
| LE:K_562 |
0.93 |
|
| LE:MOLT_4 |
0.66 |
|
| LE:RPMI_8226 |
1.09 |
|
| LE:SR |
0.12 |
| ME:LOXIMVI |
-0.91 |
| ME:MALME_3M |
0.12 |
| ME:M14 |
-0.34 |
| ME:SK_MEL_2 |
-1.22 |
| ME:SK_MEL_28 |
1.36 |
| ME:SK_MEL_5 |
-0.12 |
| ME:UACC_257 |
0.36 |
| ME:UACC_62 |
0.20 |
| ME:MDA_MB_435 |
1.02 |
| ME:MDA_N |
0.50 |
| LC:A549 |
-0.76 |
|
| LC:EKVX |
-1.01 |
|
| LC:HOP_62 |
-1.01 |
|
| LC:HOP_92 |
-0.85 |
|
| LC:NCI_H226 |
-1.79 |
|
| LC:NCI_H23 |
0.97 |
|
| LC:NCI_H322M |
0.67 |
|
| LC:NCI_H460 |
0.05 |
|
| LC:NCI_H522 |
0.56 |
|
| OV:IGROV1 |
-0.87 |
|
| OV:OVCAR_3 |
1.60 |
|
| OV:OVCAR_4 |
0.98 |
|
| OV:OVCAR_5 |
-0.93 |
|
| OV:OVCAR_8 |
-0.82 |
|
| OV:SK_OV_3 |
-0.25 |
|
| OV:NCI_ADR_RES |
-0.90 |
| PR:PC_3 |
0.32 |
|
| PR:DU_145 |
0.05 |
|
| RE:786_0 |
-0.58 |
|
| RE:A498 |
-1.08 |
|
| RE:ACHN |
-0.61 |
|
| RE:CAKI_1 |
-0.40 |
|
| RE:RXF_393 |
-0.28 |
|
| RE:SN12C |
0.06 |
|
| RE:TK_10 |
-0.59 |
|
| RE:UO_31 |
-1.18 |
|
|
|
Average log2 intensities (not mean centered)
|
|
across all probes (based on rows) in table
|
| Range |
2.92 |
| Minimum |
3.66 |
| Maximum |
6.58 |
| Average |
5.12 |
| Standard Deviation |
0.73 |
|
|
CHEK2
|
[GeneCards] |
|
Chromosome
|
22 |
| Cytogenetic band |
q12.2 |
| Start |
29083730 |
| End |
29137821 |
| Size |
54091 |
| Orientation |
- |
|
|