TCGA data analysis

Question

[aswanikrishnap1994]

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

[aswanikrishnap1994]

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.

[Kevin Blighe]

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

Answer 1

[Kevin Blighe]

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:

• GDC Legacy
• [Main] GDC Data portal

Kevin

[aswanikrishnap1994]

hi Kevin

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

[Kevin Blighe]

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

[aswanikrishnap1994]

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

[Kevin Blighe]

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)

[aswanikrishnap1994]

thank you so much kevin

[dila5458451]

hi can you help? I need to do correlation with TCGA PANCAN data set