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?
1 answer
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 http://starbase.sysu.edu.cn/targetSite.php
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Regarding point (2): welcome to the world of publicly-available expression data :)
Did you tried the browser download? https://genome-cancer.soe.ucsc.edu/proj/site/hgHeatmap/