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
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aswanikrishnap1994 •
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:
Finally, there is the data at the Genomic Data Commons, which is the primary source of TCGA data:
Kevin
hi Kevin
I took HTSeq-count data for my analysis. For DEG analysis how should i proceed with this data??
Do you not have a supervisor who is directing you how to do this?
since i am a beginner and our lab is doing this for the first time, we are not sure about the workflow.
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)
thank you so much kevin
hi can you help? I need to do correlation with TCGA PANCAN data set
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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.
Well, the data is available in 3 levels: