Method

Novel metrics for evaluating the functional coherence of protein groups via protein semantic network

Bin Zheng^1,2 and Xinghua Lu¹

¹  Department of Biostatistics, Bioinformatics and Epidemiology, 135 Cannon Street, Charleston, South Carolina 29425, USA

²  Laboratory for Functional Neurogenomics, Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Landsdowne Street, Cambridge, Massachusetts 02139, USA

author email corresponding author email

Genome Biology 2007, 8:R153doi:10.1186/gb-2007-8-7-r153

Published:	31 July 2007

Subject areas: Bioinformatics, Genome studies

Abstract

We present the metrics for assessing overall functional coherence of a group of proteins based on associated biomedical literature. A probabilistic topic model is applied to extract biologic concepts from a corpus of protein-related biomedical literature. Bipartite protein semantic networks are constructed, so that the functional coherence of a protein group can be evaluated with metrics that measure the closeness and strength of connectivity of the proteins in the network.