I will be very thankful if someone could help me. I want to retrieve miRNA-mRNA data from TCGA, data needs to be available for Cancer patient and normal for comparison. Because I want to identify differential expression of miRNA and genes in data. So please could anybody tell me how to get such type of data, and I also don't know anything about data levels in TCGA.
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written
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rajesh27071992 •
5 answers
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 are available at http://starbase.sysu.edu.cn/targetSite.php
You'll probably need to read some (or all) of the TCGA Data Primer: https://wiki.nci.nih.gov/display/TCGA/TCGA+Data+Primer
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Sean Davis
Check out OncoLand by Omicsoft: http://www.omicsoft.com/oncoland-service. It's possible to get plots like this for any two genes (miRNA, mRNA, etc.).
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matt.newman
Use TCGA-Aseemblar package in R . I use this tool for my work related to downloading GBM data for MiRAN/RNA-Seq. This package is very easy for use as well.
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always_learning
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written by jack •
Hi Rajesh,
Did you ever get an answer to your question: How To Retrieve Tcga Mirna-Mrna Data?
I'm experiencing the same problem.
Thanks in advance for helping
Benoit
You can do it by using Bioconductor tool TCGABiolink, just look the manual https://www.bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html.