Clarification on HPO Gene Set in MSigDB v2023.2.Hs "HP_ABNORMALITY_OF_GLYCOLYSIS"

[Esraa Redwan]

Dear MSigDB Team,

Greetings, 

I am currently working with MSigDB version v2023.2.Hs and identified a gene set labeled HP_ABNORMALITY_OF_GLYCOLYSIS within the archived file c5.hpo.v2023.2.Hs.symbols.gmt. However, I was unable to locate this gene set in the current MSigDB browsing interface.  

I would greatly appreciate your clarification on the following:

1. What is the current status of this gene set? Has it been deprecated, merged, or restructured in more recent releases?
2. Does this gene set have an associated MSigDB systematic identifier, or is it considered an ontology-derived annotation without a formal ID?
3. Would it be methodologically appropriate to use this gene set from the archived v2023.2.Hs release as a source for gene selection in a study?

Thank you for your time 

Best regards, 

Esraa

[Anthony Castanza]

Hi Esraa,

We dropped this set due to a change upstream in the Human Phenotype Ontology source resource.
The Abnormality of Glycolosis term was previously assigned HPO term ID:  HP:0004366 (you can find this in the archived .json file of the 2023.2 MSigDB release), however, navigating to this ID on the HPO resource site now redirects to term ID: HP:0011013 "Abnormal circulating carbohydrate concentration": https://hpo.jax.org/browse/term/HP:0004366

The current release integrated this upstream change, dropping the previous ID/name and adopting the new one:
https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/HP_ABNORMAL_CIRCULATING_CARBOHYDRATE_CONCENTRATION.html

Normally we try to keep references to rename events in the database, but due to both the resource type, and the way HPO does remappings, we aren't able to annotate changes from this resource on the gene set page version history. Also since this was due to an actual change in annotation by the upstream resource, I would not recommend using the old set as-is, and instead use the replacement set in your analysis.

Hope this helps

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego
http://gsea-msigdb.org/