Linking to GeneMANIA

The linking URL in its simplest form is http://genemania.org/#/search/<organism>/<genes> (or alternatively http://genemania.org/search/<organism>/<genes> or http://genemania.org/link?o=<tid>&g=<genes>) where:

  • <organism> : organism name or common name (e.g. human or homo_sapiens) without punctuation (e.g. bakers_yeast not baker's_yeast)
  • <tid> : NCBI taxonomy id for organism (A. thaliana=3702, C. elegans=6239, D. melanogaster=7227, H. sapiens=9606, M. musculus=10090, S. cerevisiae=4932)
  • <genes> : one or more gene symbols separated by pipes (“|”)

Examples of the simplest form:

  • one gene : http://genemania.org/link?o=3702&g=rad50
  • multiple genes : http://genemania.org/link?o=3702&g=PHYB|ELF3|COP1|SPA1|FUS9

Optional Parameters:

GeneMANIA linking supports some optional parameters (reference GeneMANIA help section on meaning of the various weighting methods):

  • m : network combining method; must be one of the following:
    • automatic_relevance : Assigned based on query genes
    • automatic : Automatically selected weighting method
    • bp : biological process based
    • mf : molecular function based
    • cc : cellular component based
    • average : Equal by data type
    • average_category : Equal by network
  • r : the number of results generated by GeneMANIA; must be a number in the range 1..100.

If no optional parameters are provided, GeneMANIA assumes the default values:m=automaticr=10.

Examples using optional parameters:

The following query runs the GeneMANIA algorithm for A. thaliana using 6 genes as input, the “average” method and returns 50 more genes:
http://genemania.org/link?o=3702&g=DET1|HY5|CIP1|CIP8|PHYA|HFR1&m=average&r=50

The following query runs the GeneMANIA algorithm for A. thaliana’s CIP1 gene using the “molecular process based” method and returns 101 genes:
http://genemania.org/link?o=3702&g=CIP1&m=bp&r=100

Invalid queries:

  • http://genemania.org/link?o=3702 : at least one gene must be specified
  • http://genemania.org/link?o=1000 : invalid taxonomy id
  • http://genemania.org/link?o=3702&g=PHYA&m=super_smart&R=50 : invalid method
  • http://genemania.org/link?o=3702&g=det1&r=1000 : results must be less than 100

Happy linking!