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phenuma_networks.zip

We provide the networks used by PhenUMA. The compresed file phenuma_networks.zip (62.5Mb) contains three tab separated files. The content of these files is listed down below. Each column of these files corresponds to a type of relationships and the score of each one is included. Therefore, each row shows all the links between two genes or diseases. If an association between two genes or disease is to score "NULL" implies that these genes or diseases are not related.

  • gene2gene.txt (343.7Mb):

    • geneX (EntrezGene)
    • geneY (EntrezGene)
    • phenotypic (HPO)
    • functional_bp (GO Biological Process)
    • functional_cc (GO Cellular Component)
    • functional_mf (GO Molecular Function)
    • ppi (protein-protein interaction from STRING)
    • metabolic (Veeramani et al.)
    • inferred_omim: relationships between genes sharing one or more OMIM diseases.
    • inferred_orpha: relationships between genes sharing one or more Orphan diseases.
    • geneXsymbol (Official Symbol)
    • geneYsymbol (Official Symnol)

  • omim2omim.txt (45.8Mb)

    • omimX (OMIM Id)
    • omimY (OMIM Id)
    • phenotypic (HPO)
    • inferred_gene: relationships between OMIM diseases sharing one or more genes.
    • omimXname: disease name
    • omimYname: disease name

  • orpha2orpha.txt (7.6Mb)

    • orphaX (Orpha Id)
    • orphaY (Orpha Id)
    • phenotypic (HPO)
    • inferred_gene: relationships between Orphan diseases sharing one or more genes.
    • orphaXname: disease name
    • orphaYname: disease name

    In Help section you can find a video tutorial about how to load these networks in Cytoscape.