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Gene 2 Pathway Predicting Pathway Membership via Domain Signatures

Functional characterization of genes is of great importance, e.g. in microarray studies. Valueable information for this purpose can be obtained from pathway databases, like KEGG. However, only a small fraction of genes is annotated with pathway information up to now. In contrast, information on contained protein domains can be obtained for a significantly higher number of genes, e.g. from the InterPro database. The R package gene2pathway implements a classification model, which for a specific gene of interest can predict the mapping to a KEGG pathway, based on its domain signature. The classifier makes explicit use of the hierarchical organization of pathways in the KEGG database. Furthermore, we take into account that a specific gene can be mapped to different pathways at the same time. The classification method produces a scoring of all possible mapping positions of the gene in the KEGG hierarchy. For signaling pathways it is even possible to forecast accurately the membership to individual pathway components.