Question: cBioPortal genetic profile id and mutational data analysis
gravatar for Nitin Sharma
23 months ago by
Nitin Sharma30
Institute for Cancer Research, Dept. of Tumor Biology, Oslo University Hospital, Oslo, Norway
Nitin Sharma30 wrote:

Dear all,

I recently started using cBioPortal and struggling to understand the terminologies used and what is the importance and application of a particular one over another and apologies for a long and naive question.

The aim of my study is to understand the mutational profile.

for the cancer study "prad_su2c_2015", I got geneticprofile as following

prad_su2c_2015_gistic Putative copy-number alterations from GISTIC prad_su2c_2015_rna_seq_mrna mRNA expression / polyA (RNA Seq RPKM) prad_su2c_2015_rna_seq_mrna_median_Zscores mRNA Expression z-Scores (RNA Seq RPKM) prad_su2c_2015_log2CNA Log2 copy-number values prad_su2c_2015_mutations Mutations prad_su2c_2015_rna_seq_capture mRNA expression / capture (RNA Seq RPKM) prad_su2c_2015_rna_seq_mrna_capture_Zscores mRNA Expression / capture z-Scores (RNA Seq capture)

Now, here is where I am confused:

  1. what is the difference between "mRNA expression / polyA" and "mRNA expression/capture"
  2. Should I use the normal score or with z-Scores?
  3. what is the difference between "Putative copy-number alterations from GISTIC" and "Log2 copy-number values" and "Relative linear copy-number values" ( Relative linear copy-number values is found in the genetic profile of "prad_tcga_pub")

I used command

mutationdata <- getMutationData(mycgds,"prad_su2c_2015_all","prad_su2c_2015_mutations",c(genes_list[1:nrow(genes_list),1]))

where c(genes_list[1:nrow(genes_list),1]) is the list of genes I am interested in.

The resulting file has function impact score but I am not able to understand what does the following characters means functional_impact_score M L NA N H

The mutation_extended results don't show Variant_Type (i.e. SNP, DNP, TNP, ONP, INS, DEL, or Consolidated)

Now when I ran the following command

mutationdata2 <- getMutationData(mycgds,"prad_su2c_2015_all","prad_su2c_2015_gistic",c(genes_list[1:nrow(genes_list),1]))

The resulting file was empty. So does it mean that there is no CNA predicted by GISTIC or I have run a wrong command?

thanks in advance

ADD COMMENTlink modified 23 months ago • written 23 months ago by Nitin Sharma30
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