Human gene set labeling error for HSD17B8_TARGET_GENES?

[Nelson Wong]

Hello,

I realized that the original study that contributed to the gene set HSD17B8_TARGET_GENES used an anti-RING2 antibody for the CHIP-seq. Unfortunately, both HSD17B8 and RNF2 were known as RING2 some point in time. However, HSD17B8 is, in fact, an enzyme that is involved in the production of estrogen, while RNF2 (RING1B or RING2) is a unit of the polycomb repressive complex. Therefore, I believe the gene set is actually RNF2-targeted genes.

I am wondering if your team is able to confirm and clarify. Thanks so much for your great work!

Kind regards,

Nelson

[Anthony Castanza]

Hi Nelson,

Thanks for reaching out to us, yes, we are aware of this issue, it is the result of an upstream annotation error in the GTRD source data. We've been in contact with them about correcting this, as well as a similar error in the set annotated as IGLV5-37 (which should be SS18-SSX fusion).

You are correct that the proper annotation for the HSD17B8_TARGET_GENES set is RING2_TARGET_GENES as indicated in the source data set: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1295081

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

--
You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/b2102a40-20aa-4561-8b56-668da7969cd1n%40googlegroups.com.

[Nelson Wong]

Hi Anthony,

Thanks so much for your prompt reply and clarification. Really appreciate your work.

Best,

Nelson

You received this message because you are subscribed to a topic in the Google Groups "gsea-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/gsea-help/W0lAuVH8GH0/unsubscribe.
To unsubscribe from this group and all its topics, send an email to gsea-help+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/CAGCeyZxg2XzCjzd2ZX-zCmiA_fTstbscPgo1Okv%2B7-xxP0srdQ%40mail.gmail.com.