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

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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).

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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.

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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?

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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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