Expression of long non-coding RNAs

Posted in TCGA data on the CGC by Xavier Mon Feb 13 2017 00:10:34 GMT+0000 (UTC)·3·Viewed 110 times

Hi! Which is the best way to get access to the expression of long non-coding RNAs? Is there any processed data (I have already checked on the case explorer) or I should reanalyze the raw data using something like Cufflinks?
Erik Lehnert
Feb 14, 2017
Hi Xavier, The easiest thing would first be to check in the level 3 expression data to see if the long, non-coding RNAs you are interested in are represented. If they are not, you can either reanalyze the data to identify your long, non-coding RNA of interest or, if these are annotated for GRCH38, wait a short period and we should be able to provide that as expression data as well. Please let me know if you have any further questions. Best, Erik
Xavier
Feb 15, 2017
Hi Erik, I'm particularly interested in the TCGA-LGG. In this project there's actually no RNAseq gene expression file, it's either junction quantification or exon quantification. Indeed, is there any way to get the expression data for all the genes that can be displayed in the case browser?? Yes, the long non-codings I'm interested are annotated in GRCH38. Best, Xavier
Erik Lehnert
Feb 15, 2017
Hi Xavier, These remapping and analysis of TCGA data to GRCH38 has been made available by the GDC, and we are currently in the process of adding this substantial addition to the CGC. We have completed the transfer and are currently building the data structure that allows you to query it on our platform. We expect to have this project completed shortly. If you'd like to send a quick e-mail to CGC@sbgenomics.com, I can reach out to you when the GRCH38 data is available. We currently do not have a tool available to get the expression of a specific gene in the TCGA datasets, but it should be fairly straightforward to parse the text files (something I can help you with if necessary). I can also be sure to pass on this feedback to our engineering team, as I agree it would be a useful feature. Best, Erik
  
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