snoRNA interaction in healthy tissues
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Message boards : Science : snoRNA interaction in healthy tissues

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andreapiazzi
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Italy
Message 2994 - Posted: 11 Nov 2022, 16:16:54 UTC

Hi to everyone!
We are a group of master student from the lab part of Data Mining at the University of Trento.

snoRNAs are a class of short non-coding RNA involved in various physiological and pathological cellular processes.
Aside from rRNA modification, new roles have been discovered and it has been shown a dysregulation in many types of cancer, observing oncogenes or tumor suppressor behaviour and a role as disease biomarkers.

Our project sets its main goal in studying snoRNAs that have been reported to be dis-regulated in cancer, and then defining which genes are causally related to them in physiological conditions, to gain knowledge regarding their interaction mechanisms and consequently their clinical applications.

From a filtered dataset containg RNA expression levels in TPM for seven healthy human tissues (breast, ovary, prostate, testis, skeletal muscle, liver, brain) in triplicate, we extracted a list of 396 expressed snoRNAs, indicated by the string snorna_ENSG0000...; we would like to expand all of these snoRNAs starting from the filtered dataset and then perform further analysis (snoRNA-host interaction, novel interaction validation, GSEA).

Falconet
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Message 2995 - Posted: 11 Nov 2022, 19:32:16 UTC - in response to Message 2994.
Last modified: 11 Nov 2022, 19:34:16 UTC

Yes, I got a few of these in the morning.
Short ones.
____________

entity
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Message 2996 - Posted: 11 Nov 2022, 20:52:44 UTC - in response to Message 2995.

They produce about 100 times as much data as the other WUs (about 8k vs 800K). Is this what is causing the external filesystem issues?

Profile valterc
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Message 2997 - Posted: 11 Nov 2022, 22:40:56 UTC - in response to Message 2996.

The larger output file size for these workunits is normal.
The file system is behaving weirdly, my guess is that the problem is not the I/O throughput but something related to the i-nodes or the net interface. It takes minutes just to delete a single file...


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