You have a set of genes and would like to know if those genes are enriched for a pathway, a Gene Ontology term, or other types of annotations. This pipeline tests your gene set for enrichment against a large compendium of annotations pre-loaded into KnowEnG. You may use a standard statistical test or choose a Knowledge Network-guided mode that uses the DRaWR, NetPath or MetaGeneRank algorithms.
Technical footnote: DRaWR uses discriminative random walk with restarts on a heterogeneous graph, NetPath is based on embedding gene and property nodes into a common low-dimensional vector space, and MetaGeneRank uses meta-paths to identify connectivity patterns characteristic of the gene set before using classification techniques with these patterns.
Publication: Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks.
Charles Blatti and Saurabh Sinha
Bioinformatics, Volume 32, Issue 14, 15 July 2016, Pages 2167–2175, https://doi.org/10.1093/bioinformatics/btw151