Question: Get relative gene expression levels of a gene (for example, TP53) across all (or most) TCGA cancer samples
2
gravatar for wcc957
4.1 years ago by
wcc95720
United States
wcc95720 wrote:

I am interested in looking for relative gene expression level of a gene (such as TP53) across all cancer samples to get some senses of what cancer samples have greater expression of the gene. I found similar results provided by BioGPS (http://biogps.org/#goto=genereport&id=7157) and starBase2.0 (http://starbase.sysu.edu.cn/viewGeneInfo.php?table=ceRNANetworksAll&database=hg19&name=tp53). Are there any similar services/databases providing relative gene expression levels only based on The Cancer Genome Atlas (TCGA) data? Thanks!

ADD COMMENTlink modified 4.0 years ago by Malachi Griffith17k • written 4.1 years ago by wcc95720
1
gravatar for Malachi Griffith
4.0 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

I believe you can do this with the TCGA data portal using the 'Data Matrix' option:

https://tcga-data.nci.nih.gov/tcga/tcgaDownload.jsp

You might need to do it for each cancer type individually though.  And you will obtain an archive of processed expression files that you will have to do some parsing of...

 

ADD COMMENTlink written 4.0 years ago by Malachi Griffith17k

Thank you, Malachi. 

ADD REPLYlink written 4.0 years ago by wcc95720
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