Question about M5 collection

[Liu Zhe]

Hi ,

I am a rookie of GSEA. 

I was trying to perform GSEA in matlab by using the M5 collection downloaded from MSigDB.

The description of M5 collection of link said 'ontology terms that produced gene sets with fewer than 5 members have been omitted.'

(https://www.gsea-msigdb.org/gsea/msigdb/mouse/collection_details.jsp)

But I find that there are a lot of GO (around 1500 GOs) in m5 collection, which has 3 or 4 members.

Why this occurs?

I want to set a filter rule of GOs member for GSEA of M5 collection, should the rule be same as M5 collection(5-2000)?

[Anthony Castanza]

Hello,

The human and mouse GO collections are prepared to the same specifications. If there are sets on the website that contain fewer than 5 members I would generally consider this a bug in our build procedure.

If the sets are only showing up as having fewer than 5 members after running GSEA in your GSEA results this would likely have a different cause, specifically an interaction between the sets gene universe filtering and a lower than typical min size threshold in GSEA. We don't provide or support a Matlab implement of GSEA so I'm not sure if it has non-standard parameters here.

Could you perhaps provide the names of a couple sets where you're observing this?

Thanks,

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

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