Question: Gene set enrichment from cbio portal data
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gravatar for kulani.s91
19 months ago by
kulani.s910
kulani.s910 wrote:

I have a dataset of copy number alteration data from different samples of prostrate cancer from cbioportal.org. A sample of the table is below:

Gene_ID    MO_1008  MO_1012    MO_1013    MO_1014
A1BG       0        0          1          0
A1CF       2        0         -1          0
PTEN       0        0          0          1
A2ML1      0        0          0          1
GPA33      -1      -1          0          0
A4GNT      1        0          1          1

I would like to conduct a gene set enrichment analysis for the genes using this dataset. Could I know the steps to perform the analysis using this data?

R • 427 views
ADD COMMENTlink modified 19 months ago by RamRS26k • written 19 months ago by kulani.s910

To what does the data relate? From which section on cBioPortal did you obtain it? Have you already searched for help on gene enrichment... ? - there are, literally, dozens of programs.

ADD REPLYlink written 19 months ago by Kevin Blighe56k

I got this data by combining three prostate cancer studies in cbioportal. I found some libraries in R to do gene set enrichment. But I do not know how to convert my dataset to match the required input for those libraries.

ADD REPLYlink modified 19 months ago • written 19 months ago by kulani.s910

Put yourself in my shoes - I have no idea to which "libraries" you are referring. I neither have any idea how you merged these prostate cancer datasets.

ADD REPLYlink modified 19 months ago • written 19 months ago by Kevin Blighe56k
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