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BaderLab / EnrichmentMapApp

The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
http://apps.cytoscape.org/apps/enrichmentmap
GNU Lesser General Public License v2.1
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July gene sets (at least the Human ones) are missing the genes #490

Closed toddajohnson closed 2 years ago

toddajohnson commented 2 years ago

I had previously used Human_GO_AllPathways_no_GO_iea_April_01_2022_symbol.gmt and today downloaded the July 2022 version Human_GO_AllPathways_no_GO_iea_July_01_2022_symbol.gmt.txt, but the gene symbols in the July file seem to be missing. Also missing in Human_GOBP_AllPathways_no_GO_iea_July_01_2022_symbol.gmt, which I first downloaded after realizing it's the recommended file.

For instance July: PROTEIN CITRULLINATION%BIOCYC%PWY-4921 protein citrullination

April: PROTEIN CITRULLINATION%HUMANCYC%PWY-4921 protein citrullination PADI6 PADI3 PADI2 PADI4 PADI1

risserlin commented 2 years ago

Thanks for reporting. Looks like the identifier conversion might be down. The identifiers are only found for the original ID the data was downloaded in. I will rebuild and let you know when the latest fixed version is up. Thanks,

risserlin commented 2 years ago

Fixed (for now :) , unfortunately it is a bigger issue ) The July genesets have been updated and are available here - https://download.baderlab.org/EM_Genesets/July_05_2022/