How To Retrieve Tcga Mirna-Mrna Data

Question

[rajesh27071992]

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.

[derijard]

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

[Nitish Mishra]

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.

Answer 1

[lsp03yjh]

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

Answer 2

[Sean Davis]

You'll probably need to read some (or all) of the TCGA Data Primer: https://wiki.nci.nih.gov/display/TCGA/TCGA+Data+Primer

Answer 3

[Na Sed]

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.

Answer 4

[matt.newman]

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.).

Answer 5

[always_learning]

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.