How To Retrieve Tcga Mirna-Mrna Data
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8.0 years ago

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's and genes in data. So plz could anybody tell me how to get such type of data, and i also dont know nothing about data levels in TCGA.

mirna • 8.6k views
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Hi Rajesh,

Did you ever get an answer to your question : How To Retrieve Tcga Mirna-Mrna Data ?

I'm experiencing the same problem.

Txs in advance for helping

Benoit

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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.

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7.9 years ago
lsp03yjh ▴ 810

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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8.0 years ago

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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6.8 years ago
Na Sed ▴ 310

When you filter data out, you can select two types of miRNA expression as well as mRNA expression. Then you can see some samples have both types of data. You can try it for Breast cancer.

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6.5 years ago
matt.newman ▴ 170

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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6.4 years ago
always_learning ★ 1.1k

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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