How to get all Long non-coding RNA expression data from TCGA

Question

[Mike]

Hi all,

Is TCGA contains expression data for all Long non-coding RNA? If so, then how to get them.

Thanks,

[Mike]

I have downloaded Long nc RNA expression data from TANRIC (log2) for particular gene and now I want to scatter plot between lncRNA expression and mRNA expression. what would be the best way to plot them?

Thanks

[EagleEye]

What do you mean by mRNA expression? mRNA of what !!!

[Mike]

I want to plot and calculate correlation between Linc00589 & EGFR. for Linc00589 I have lnc RNA expression data from (TANRIC) and for EGFR mRNA expression from TCGA.

[EagleEye]

Why don't you use Linc00589 & EGFR expression data from same source. Like in your case use TCGA expression data (I guess it will have expression for both protein coding and lncRNAs too) and plot the correlation between these two transcripts.

[Mike]

Thanks

Yes, I also thinkng similar way and plotted expression, but I have one more gene "CASC11" which is not present in TCGA, So can I plot this with EGFR using different sources (TCGA & TANRIC)??

[Saber HQ]

Actually, the lncRNA expressions in TANRIC website are from TCGA database.

Answer 1

[EagleEye]

http://ibl.mdanderson.org/tanric/_design/basic/index.html

http://mitranscriptome.org

https://www.synapse.org/#!Synapse:syn300013/files/

[Mike]

Thanks ,

Sorry , I forgot to mention about "Long non-coding RNA". Is this for Long non-coding RNA??

[EagleEye]

Yes TANRIC and miTranscriptome covers Long non-coding RNAs.

Synapse project covers all type of RNAs, use available annotations like Gencode to extract only lncRNAs from synapse.

[Mike]

Thanks, for your quick reply, highly appreciated