Question: TCGA data analysis
0
gravatar for aswanikrishnap1994
11 days ago by
aswanikrishnap19940 wrote:

hi, i have a set of genes involved in particular function and want to compare across all the cancer samples in TCGA in order to find some correlation. I am completely new to this and have no idea how to proceed further with TCGA data

ADD COMMENTlink modified 11 days ago • written 11 days ago by aswanikrishnap19940

Thank you Kevin for the suggestion. But i guess TCGA data is not open access now, so i won't be able to download the dataset. For that i am currently using UCSC XENA.

ADD REPLYlink written 11 days ago by aswanikrishnap19940
1

Well, the data is available in 3 levels:

  • Level 1: raw data; controlled access
  • Level 2: processed data; controlled access
  • Level 3: processed data; open access
ADD REPLYlink written 10 days ago by Kevin Blighe45k
2
gravatar for Kevin Blighe
11 days ago by
Kevin Blighe45k
Kevin Blighe45k wrote:

If you simply want a quick way to look up a few genes, then your best option is cBioPortal: http://www.cbioportal.org/

If you are prepared to do some processing of the data yourself, then you can obtain raw and/or normalised data from various sources, popular ones being:

  • UCSC's Xena browser
  • Broad Institute's FireBrowse (also has in-built correlation tool)

Finally, there is the data at the Genomic Data Commons, which is the primary source of TCGA data:

Kevin

ADD COMMENTlink modified 9 days ago • written 11 days ago by Kevin Blighe45k

hi Kevin

I took HTSeq-count data for my analysis. For DEG analysis how should i proceed with this data??

ADD REPLYlink modified 7 days ago • written 7 days ago by aswanikrishnap19940

Do you not have a supervisor who is directing you how to do this?

ADD REPLYlink written 6 days ago by Kevin Blighe45k

since i am a beginner and our lab is doing this for the first time, we are not sure about the workflow.

ADD REPLYlink written 6 days ago by aswanikrishnap19940

Okay, there is some help in the DESeq2 vignette: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#htseq-count-input

Basically, the HTseq files contain raw counts. These will be input to R where DESeq2 will normalise them. Eventually, you will be able to perform differential expression analysis. Everything that you need is in the DESeq2 vignette (link above)

ADD REPLYlink written 6 days ago by Kevin Blighe45k
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