I want to analyze one gene across three cancer types - bladder, breast and colon to find out its role in cancer prognosis if any. Is there any online resource/ database is available which I can use for this purpose. I found http://bioinformatica.mty.itesm.mx:8080/Biomatec/SurvivaX.jsp but it is hard to predict and cannot select more than one datasets.
The NIH Cancer Genome Atlas (TCGA) has various data for 20.5k genes and 31 cancer tissue types, with normal and tumor subtypes for most tissues. I wrote a browser for normalized per-gene expression data which allows at-a-glance comparison of relative RNA abundance in selected tissues and either a "single" or "gallery" listing of a gene- or genes-of-interest, resp.
I have few clarifications about this TCGA expression browser
1. It takes level 3 TCGA data or some other level.
2. The figure shows TPM, I was wondering how the RNA seq data has bee finally analyzed in the backend. IS it RSEM or RPKM level analysis
3. Raw CSV will output raw read count data or it has been preprocessed in some way.