Question: Obtaining the CNA data
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gravatar for shivangi.agarwal800
12 months ago by
shivangi.agarwal80070 wrote:

Hi

I want to obtain the CNA data for particular cancer type. I downloaded the data from Gistic and Cosmic, but I didnot get the data in the form I want. I want the data cancerwise, patientwise and genewise, like we get the expression data.

From Gistic, I downloaded different files as: gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.mage-tab.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.mage-tab.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.Level_4.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.Level_4.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.aux.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.aux.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.mage-tab.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.mage-tab.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2016012800.0.0

Please suggest

Regards

Shivangi

cancer cna • 361 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by shivangi.agarwal80070

Hello shivangi.agarwal800!

What have you tried? Please show us you have invested some effort and I will reopen the question. You can edit your question and add relevant details, then reply to this comment to alert me of the edit.

ADD REPLYlink modified 12 months ago • written 12 months ago by RamRS25k

I downloaded the data from Gistic and Cosmic, but I didnot get the data in the form I want. I want the data cancerwise, patientwise and genewise, like we get the expression data.

From Gistic, I downloaded different files as: gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.mage-tab.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.mage-tab.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.Level_4.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.Level_4.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.aux.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.aux.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.mage-tab.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.mage-tab.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2016012800.0.0

ADD REPLYlink written 12 months ago by shivangi.agarwal80070

Please edit your question and add this information there.

ADD REPLYlink written 12 months ago by RamRS25k

Have edited the original question

ADD REPLYlink written 12 months ago by shivangi.agarwal80070

I've reopened your question.

ADD REPLYlink written 12 months ago by RamRS25k
0
gravatar for shivangi.agarwal800
12 months ago by
shivangi.agarwal80070 wrote:

Hi

While unzipping TP.CopyNumberLowPass_Gistic2.aux.2016012800.0.0.tar.gz, there is GDAC_Gistic2Report_22529547_broad_data_by_genes.txt file. While looking into the contents, I got as

GDAC_Gistic2Report_22529547_broad_data_by_genes.txt | cut -f-15 Gene Symbol Locus ID Cytoband TCGA-3C-AAAU-01A-11D-A41E-01 TCGA-3C-AALI-01A-11D-A41E-01 TCGA-3C-AALJ-01A-31D-A41E-01 TCGA-3C-AALK-01A-11D-A41E-01 TCGA-4H-AAAK-01A-12D-A41E-01 TCGA-5L-AAT0-01A-12D-A41E-01 TCGA-5L-AAT1-01A-12D-A41E-01 TCGA-5T-A9QA-01A-11D-A41E-01 TCGA-A1-A0SB-01A-11D-A141-01 TCGA-A1-A0SD-01A-11D-A111-01 TCGA-A1-A0SE-01A-11D-A087-01 TCGA-A1-A0SF-01A-11D-A141-01

ACAP3 116983 1p36.33 0.000 -0.518 -0.240 0.000 0.000 0.000 0.000 -0.647 0.000 0.000 0.000 0.322

I did not understand why there are different values (0.00, -0.518, -0.240, 0.000) for different patients when Gene Symbol,Locus ID and Cytoband are same. Can anyone suggest??

Regards

ADD COMMENTlink written 12 months ago by shivangi.agarwal80070

Hello,

Is this an answer to your top level question?

ADD REPLYlink written 12 months ago by RamRS25k
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