Guan Lab

Department of Computational Medicine & Bioinformatics
Wed, 11/06/2013 - 10:14 -- gl_admin
TitleFunctional knowledge transfer for high-accuracy prediction of under-studied biological processes.
Publication TypeJournal Article
Year of Publication2013
AuthorsPark CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG
JournalPLoS Comput Biol
Volume9
Issue3
Paginatione1002957
Date Published2013
ISSN1553-7358
Abstract

A key challenge in genetics is identifying the functional roles of genes in pathways. Numerous functional genomics techniques (e.g. machine learning) that predict protein function have been developed to address this question. These methods generally build from existing annotations of genes to pathways and thus are often unable to identify additional genes participating in processes that are not already well studied. Many of these processes are well studied in some organism, but not necessarily in an investigator's organism of interest. Sequence-based search methods (e.g. BLAST) have been used to transfer such annotation information between organisms. We demonstrate that functional genomics can complement traditional sequence similarity to improve the transfer of gene annotations between organisms. Our method transfers annotations only when functionally appropriate as determined by genomic data and can be used with any prediction algorithm to combine transferred gene function knowledge with organism-specific high-throughput data to enable accurate function prediction. We show that diverse state-of-art machine learning algorithms leveraging functional knowledge transfer (FKT) dramatically improve their accuracy in predicting gene-pathway membership, particularly for processes with little experimental knowledge in an organism. We also show that our method compares favorably to annotation transfer by sequence similarity. Next, we deploy FKT with state-of-the-art SVM classifier to predict novel genes to 11,000 biological processes across six diverse organisms and expand the coverage of accurate function predictions to processes that are often ignored because of a dearth of annotated genes in an organism. Finally, we perform in vivo experimental investigation in Danio rerio and confirm the regulatory role of our top predicted novel gene, wnt5b, in leftward cell migration during heart development. FKT is immediately applicable to many bioinformatics techniques and will help biologists systematically integrate prior knowledge from diverse systems to direct targeted experiments in their organism of study.

DOI10.1371/journal.pcbi.1002957
Alternate JournalPLoS Comput. Biol.
PubMed ID23516347
PubMed Central IDPMC3597527
Grant ListR01 GM071966 / GM / NIGMS NIH HHS / United States
R01 HG005998 / HG / NHGRI NIH HHS / United States
T32 HG003284 / HG / NHGRI NIH HHS / United States