Mouse-GEM data

This directory contains datasets that were used for the generation and curation of Mouse-GEM. The files and their contents are briefly summarized below.

• human2MouseOrthologs.tsv: The human-mouse ortholog pairs downloaded from the Alliance of Genomes Resources using following code:

curl -X \
GET "https://www.alliancegenome.org/api/homologs/9606/10090?filter.stringency=stringent&limit=50000&page=1" \
-H  "accept: application/json" | \
jq -r \
'["fromGeneId", "fromSymbol", "toGeneId", "toSymbol", "best", 
"bestReverse", "methodCount", "totalMethodCount"], (.results[] | 
[.gene["id"], .gene["symbol"], .homologGene["id"], .homologGene["symbol"], 
.best, .bestReverse, .methodCount, .totalMethodCount]) 
| @tsv' > human2MouseOrthologs.tsv

• mouseSpecificMets.tsv and mouseSpecificRxns.tsv: The curated metabolic network that is not part of human metabolism but specific to mouse.
• MGI_gene_ID_mapping.tsv: The information of gene ID mapping between various identifiers that was extracted from the MGI_Gene_Model_Coord.rpt file in MGI.
• MSigDB: The mouse gene sets that were retrieved from the Molecular Signatures Database and followed by replacing human genes with the ortholog counterparts of mouse.