file of highest differentially expressed lncRNA with cancer/lineage and tissue information

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Brendan Miller

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Sep 23, 2015, 10:56:57 PM9/23/15
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On the MiTranscriptome website, the Transcript Browser currently shows information for the most differentially expressed lncRNAs. Is this information also available as a downloadable file? Specifically, I would like a file that contains the transcript name, association (cancer and/or lineage), tissue type, and expression percentile. If not, is there a straightforward way to get this information into a file? 


What I've done so far and where I am stuck:
I have downloaded the Assembly BED file, and the FPKM Expression file, however these use the T00... transcript identifiers instead of the Name in the Transcript Browser. I was able to download the bb (bigbed) file of the top differentially expressed transcripts from UCSC and using this information I can convert between the two different assembly identifiers. However, with respect to assigning a differentially expressed transcript to a specific tissue type and association, I don't see a feasible way to do this besides manually going through all 16000+ entries in the Transcript Browser, which is highly impractical. From the FPKM file, I am unclear how to recapitulate the SSEA results, and the posted SSEA and Assembler code on the website is not very clear, either.

Any help or suggestions would be greatly appreciated.

Thanks

Yashar Niknafs

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Sep 28, 2015, 4:20:17 PM9/28/15
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Hi Brendan, 

Thanks for sending me an email. I'll email you this file. 

Best, 
Yashar 

Brendan Miller

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Sep 28, 2015, 10:12:06 PM9/28/15
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Got it! Thanks a bunch, I really appreciate it.

anaklaud...@gmail.com

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Nov 1, 2015, 8:00:41 AM11/1/15
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Dear Yashar

I have a similar query to Brendan and was wondering if you could please also send me a file with the DE lncRNAs? Thank you!!

Best Wishes

Ana

Yashar Niknafs

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Dec 4, 2015, 6:56:02 PM12/4/15
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Not a problem. Will do shortly. 

-Yashar 

jan...@ganitlabs.in

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Jul 13, 2016, 6:09:25 AM7/13/16
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Hello Yashar,

I was looking for the same information and came across this thread. Is it possible for you to email me this file as well?

Thanks,

Janani

Yashar Niknafs

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Jul 13, 2016, 10:21:30 AM7/13/16
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