Defining functional distance using manifold embeddings of gene ontology annotations.

ABSTRACT: Although rigorous measures of similarity for sequence and structure are now well established, the problem of defining functional relationships has been particularly daunting. Here, we present several manifold embedding techniques to compute distances between Gene Ontology (GO) functional annotations and consequently estimate functional distances between protein domains. To evaluate accuracy, we correlate the functional distance to the well established measures of sequence, structural, and phylogenetic similarities. Finally, we show that manual classification of structures into folds and superfamilies is mirrored by proximity in the newly defined function space. We show how functional distances place structure-function relationships in biological context resulting in insight into divergent

SUBMITTER: Lerman G 

PROVIDER: S-EPMC2040899 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature