Question: List of TCGA genes differentially expressed in normal versus tumor
0
gravatar for jamespower
23 months ago by
jamespower50
jamespower50 wrote:

Hi,

I am looking for a gene list with differentially expressed genes in a particular tissue, using normal versus tumor samples (for example as reported in https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071462#s3).

The TCGA website has RNA-Seq data on tumor samples, but I was just looking for the reported gene list, not to do analysis myself.

Where can I find this?

Thank you

rna-seq tcga • 1000 views
ADD COMMENTlink modified 9 months ago • written 23 months ago by jamespower50

Hi James, RNA-seq / gene expression was not a primary focus of the TCGA. The data that is available at Genomics Data Commons (GDC) does not include any differential expression results for tumour versus normal. I am neither aware of any third party web-site that has such data. Your best bet is to re-analyse it yourself. I began doing this last year and it would only have taken 1 week to re-analyse the main cancers, however, I am an experienced user of TCGA data. What is stopping you from going ahead to re-analyse it? Time constraint?

ADD REPLYlink modified 9 months ago • written 23 months ago by Kevin Blighe69k

Thank you Kevin for your reply. Yes, time constrains, and the fact that I was hoping there were gene lists available already, since it seems like a very common and possibly simple analysis that doesn't need to be re-done by everyone...

ADD REPLYlink written 23 months ago by jamespower50

I have just done another quick search and cannot find anything. Another issue is that not many normal tissues had RNA-seq performed. I recall that some cancers had 0 normal RNA-seq samples. Breast cancer (BRCA), which is the largest cohort, has 107 normal RNA-seq samples, I believe. I think that colon or lung only had ~15 or so.

If I had the data on hand I would share it with you, but don't have it unfortunately. Firebrowse has the count matrices in RSEM and other formats: http://firebrowse.org/

RSEM can be input to DESeq2 via tximport.

ADD REPLYlink written 23 months ago by Kevin Blighe69k
0
gravatar for jamespower
9 months ago by
jamespower50
jamespower50 wrote:

To follow-up if useful to others, I found three websites that will do this automatically:

http://gepia.cancer-pku.cn/index.html

xena.ucsc

http://www.cbioportal.org/

The gepia website seems great because it allows to do a bulk comparison, the others seem to be focused on a "by gene" comparison.

ADD COMMENTlink modified 9 months ago • written 9 months ago by jamespower50
1

Just to clarify: these web-sites that you list will perform differential expression comparisons for the user via a web GUI?

ADD REPLYlink written 9 months ago by Kevin Blighe69k
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