gamma-AM is the implementation of a novel method for inferring biological function for a set B of genes with previously unknown function, given a set A of genes with well-known semantic information. It receives one file with gene expression data for each set, and also a semantic distance matrix for A set. Default values for the gamma parameter are 0.95 for yeast specie and 0.75 for arabidopsis specie. A custom value can be set for other species. It provides two outputs: a .csv file with detailed information for each gene on Cluster ID, set, gene-centroid, gene name and a http link to the GO graph corresponding to the inferred terms for the cluster; and a .html file with gene name and a link to the GO graph corresponding to the inferred terms for the cluster.
Contact: Georgina Stegmayer