Question: Help On Getting Data From Tcga
gravatar for jack
7.1 years ago by
jack490 wrote:

Hi all,

I'm trying to get data for mRNA-miRNA expression RNA-seq data (both measured in one sample) from TCGA , but when I download and read it, there are some problems:

1) for one sample there is lot's of txt file on it

2) it's not really clear what is the expression value(should I take raw count or ..)

3) is there any tool to put all the expression value of the genes and sample in one matrix ?

bioinformatics tcga • 3.1k views
ADD COMMENTlink modified 7.1 years ago by lsp03yjh800 • written 7.1 years ago by jack490

Regarding point (2): welcome to the world of publicly-available expression data :)

ADD REPLYlink written 7.1 years ago by Neilfws49k

Did you tried the browser download?

ADD REPLYlink written 7.1 years ago by Jimbou820
gravatar for lsp03yjh
7.1 years ago by
lsp03yjh800 wrote:

You can use starBase Pan-Cancer Analysis Platform . starBase Pan-Cancer Analysis Platform is designed for deciphering Pan-Cancer Networks of lncRNAs, miRNAs, ceRNAs and RNA-binding proteins (RBPs) by mining clinical and expression profiles of 14 cancer types (>6000 samples) from The Cancer Genome Atlas (TCGA) Data Portal (all data available without limitations).

starBase generated Pan-Cancer networks of CLIP-Seq experimentally supported miRNA-lncRNA and miRNA-mRNA interactions.

Pan-Cancer miRNA-mRNA interactions can be available at

ADD COMMENTlink written 7.1 years ago by lsp03yjh800
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