Re: Co-Expression Analysis and RNA count data

[Kadie Hudson]

I was able to find the entry in the data file using an alternate name. Apologies for the premature email!

On Fri, Nov 18, 2022 at 3:01 PM Kadie Hudson <rce...@virginia.edu> wrote:

Hi,

My name is Kadie and I am trying to run some bioinformatic analysis using the available data that I pulled from the cBioPortal web page. The study I am referring to is Brain Lower Grade Glioma (TCGA, Firehose Legacy) and the data file I am referring to is data_mrna_seq_v2_rsem.txt

Using co-expression analysis on the web interface I can see that SERTAD4BP is accessible and is expressed in many samples within this study. However, when I look for SERTAD4BP in the data file, I cannot find any entries for that gene.

This particular gene produces a long non-coding RNA so I am wondering if those counts are stored in an alternate data file and if so, which one? Alternatively I am wondering if this gene is listed under an alternate name in the data file than what is shown on the co-expression interface (SERTAD4BP) and if so, which one?

If you have any information about this or could direct me towards who to ask, I would greatly appreciate it.

Thank you!

--

Kadie Hudson

B.S. Genetics | MIC Graduate Student

University of Virginia | Abounader Lab

rce...@virginia.edu | 540.235.1373

--

Kadie Hudson

B.S. Genetics | MIC Graduate Student

University of Virginia | Abounader Lab

rce...@virginia.edu | 540.235.1373

[Kadie Hudson]

[debr...@mskcc.org]

Great! Glad you found it! Thanks!

Ino

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From: 'Kadie Hudson' via cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Sent: Friday, November 18, 2022 3:15:24 PM
To: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: [EXTERNAL] [cbioportal] Re: Co-Expression Analysis and RNA count data

 

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