Obtaining the CNA data

Question

[shivangi.agarwal800]

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

[Ram]

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.

[shivangi.agarwal800]

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

[Ram]

Please edit your question and add this information there.

[shivangi.agarwal800]

Have edited the original question

[Ram]

I've reopened your question.

Answer 1

[shivangi.agarwal800]

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

[Ram]

Hello,

Is this an answer to your top level question?