Question: How To Retrieve Tcga Mirna-Mrna Data
3
gravatar for rajesh27071992
6.6 years ago by
rajesh2707199230 wrote:

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 • 8.1k views
ADD COMMENTlink modified 5.1 years ago by always_learning1.0k • written 6.6 years ago by rajesh2707199230

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

ADD REPLYlink written 5.7 years ago by derijard0

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.

ADD REPLYlink written 4.3 years ago by Nitish Mishra30
3
gravatar for lsp03yjh
6.6 years ago by
lsp03yjh800
China
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 http://starbase.sysu.edu.cn/targetSite.php

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by lsp03yjh800
1
gravatar for Sean Davis
6.6 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

You'll probably need to read some (or all) of the TCGA Data Primer:

https://wiki.nci.nih.gov/display/TCGA/TCGA+Data+Primer

ADD COMMENTlink written 6.6 years ago by Sean Davis26k
0
gravatar for Na Sed
5.5 years ago by
Na Sed300
United States
Na Sed300 wrote:

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.

ADD COMMENTlink written 5.5 years ago by Na Sed300
0
gravatar for matt.newman
5.2 years ago by
matt.newman150
United States
matt.newman150 wrote:

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.).

ADD COMMENTlink written 5.2 years ago by matt.newman150
0
gravatar for always_learning
5.1 years ago by
always_learning1.0k
Doha, Qatar
always_learning1.0k wrote:

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. 

ADD COMMENTlink written 5.1 years ago by always_learning1.0k
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