Problem in GTRD gene sets?

[John Bruce]

While doing a GSEA, I came across two gene sets derived from GTRD that were puzzling to me:

These gene sets are from "c3.tft.gtrd.v2023.2.Hs.symbols.gmt" available on https://www.gsea-msigdb.org :

• HSD17B8_TARGET_GENES.  The name implies that HSD17B8 is a transcription factor, but I cannot find any report that this enzyme, Hydroxysteroid 17-Beta Dehydrogenase 8, binds chromatin.
• IGLV5_37_TARGET_GENES: The gene IGLV5_37 encodes Immunoglobulin Lambda Variable 5-37, which is not a DNA-binding protein.  I wonder whether this list belongs to a negative control in chromatin immunoprecipitation experiments.

Might there be a mistake in the preparation of these gene sets or am I misunderstanding something?

John Bruce, Ph.D.
Sr. Data Scientist

BPGbio

 

[Anthony Castanza]

Hi John,

I suspect that this is an annotation error in the upstream GTRD database where we pull this dataset. For HSD17B8 it appears that the data is originating from this experiment:

http://gtrd.biouml.org/#!table/gtrd_current.experiments/Details/ID=EXP054277

http://gtrd.biouml.org/#!table/gtrd_current.experiments/Details/ID=EXP054282

With this dataset reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1295092

and this publication: https://pubmed.ncbi.nlm.nih.gov/24485159/

And I'm not sure how they derived the annotation for HSD17B8

As for IGLV5.37, it appears to be referencing the following: http://gtrd.biouml.org/#!table/gtrd_current.experiments/Details/ID=EXP048067

which is incorrectly associating the V5 tag used on the SS18-SSX fusion protein in this experiment: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108025

from this study: https://pubmed.ncbi.nlm.nih.gov/29861296/

Sorry about the annotation error here! I'll submit a report to the GTRD maintainers to hopefully get this corrected!

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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