maayanlab / g2n Goto Github PK

Clarke DJB and Kuleshov MV, Schilder BM, Torre D, Duffy ME, Keenan AB, Lachmann A, Feldmann AS, Gundersen GW, Silverstein MC, Wang Z, Ma�ayan A. eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. Nucleic Acid Research Nucleic Acids Research, Volume 46, Issue W1: 171�179 (2018)

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Although not on PubMed this reference can be added to the references column:
https://www.liebertpub.com/doi/abs/10.1089/152791601750294344?journalCode=bsi

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Enter a list of mammalian genes or proteins in Entrez gene symbol format to receive results of a protein–protein interactions (PPI) subnetwork that connects the enriched genes/proteins with known protein-protein interactions using Genes2Networks (G2N). G2N connects you input list of genes/proteins using the shortest path algorithms using known PPI from the selected databases.

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Possible other formats are:
SIG file
Text file
BioPAX

From here you can download a command line standalone version of G2N in JAR format.

General format on how to run the G2N command line tool:
java -jar G2N.jar input output.sig [backgroundSigFiles...]

Example of how to run the G2N command line tool: