Combining Hierarchical and Associative Gene Ontology Relations with Textual Evidence in Estimating Gene and Gene Product Similarity

Journal Article · Thu Mar 01 04:00:00 EST 2007 · IEEE Transactions on NanoBioscience, 6(1):51-59

DOI:https://doi.org/10.1109/TNB.2007.891886· OSTI ID:902678

Sanfilippo, Antonio P; Posse, Christian; Gopalan, Banu; Riensche, Roderick M; Beagley, Nathaniel; Baddeley, Bob L; Tratz, Stephen C; Gregory, Michelle L

Gene and gene product similarity is a fundamental diagnostic measure in analyzing biological data and constructing predictive models for functional genomics. With the rising influence of the Gene Ontology, two complementary approaches have emerged where the similarity between two genes or gene products is obtained by comparing Gene Ontology (GO) annotations associated with the genes or gene products. One approach captures GO-based similarity in terms of hierarchical relations within each gene subontology. The other approach identifies GO-based similarity in terms of associative relations across the three gene subontologies. We propose a novel methodology where the two approaches can be merged with ensuing benefits in coverage and accuracy, and demonstrate that further improvements can be obtained by integrating textual evidence extracted from relevant biomedical literature.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 902678
• Report Number(s): PNNL-SA-51075
• Journal Information: IEEE Transactions on NanoBioscience, 6(1):51-59, Journal Name: IEEE Transactions on NanoBioscience, 6(1):51-59 Journal Issue: 1 Vol. 6
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
ACCURACY
BLAST
FUNCTIONALS
GENES
Gene Ontology
GoPubMed
gene product similarity
ontology alignment