Guan Lab

Department of Computational Medicine & Bioinformatics
Wed, 11/06/2013 - 10:23 -- gl_admin
TitleA critical assessment of Mus musculus gene function prediction using integrated genomic evidence.
Publication TypeJournal Article
Year of Publication2008
AuthorsPeña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WKyu, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GNing, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph, iv Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP
JournalGenome Biol
Volume9 Suppl 1
Date Published2008
KeywordsAlgorithms, Animals, Mice, Proteins

BACKGROUND: Several years after sequencing the human genome and the mouse genome, much remains to be discovered about the functions of most human and mouse genes. Computational prediction of gene function promises to help focus limited experimental resources on the most likely hypotheses. Several algorithms using diverse genomic data have been applied to this task in model organisms; however, the performance of such approaches in mammals has not yet been evaluated.RESULTS: In this study, a standardized collection of mouse functional genomic data was assembled; nine bioinformatics teams used this data set to independently train classifiers and generate predictions of function, as defined by Gene Ontology (GO) terms, for 21,603 mouse genes; and the best performing submissions were combined in a single set of predictions. We identified strengths and weaknesses of current functional genomic data sets and compared the performance of function prediction algorithms. This analysis inferred functions for 76% of mouse genes, including 5,000 currently uncharacterized genes. At a recall rate of 20%, a unified set of predictions averaged 41% precision, with 26% of GO terms achieving a precision better than 90%.CONCLUSION: We performed a systematic evaluation of diverse, independently developed computational approaches for predicting gene function from heterogeneous data sources in mammals. The results show that currently available data for mammals allows predictions with both breadth and accuracy. Importantly, many highly novel predictions emerge for the 38% of mouse genes that remain uncharacterized.

Alternate JournalGenome Biol.
PubMed ID18613946
PubMed Central IDPMC2447536
Grant ListHG0017115 / HG / NHGRI NIH HHS / United States
HG002273 / HG / NHGRI NIH HHS / United States
HG003224 / HG / NHGRI NIH HHS / United States
HG004098 / HG / NHGRI NIH HHS / United States
HG004233 / HG / NHGRI NIH HHS / United States
HL81341 / HL / NHLBI NIH HHS / United States
LM07994-01 / LM / NLM NIH HHS / United States
P50 GM071508 / GM / NIGMS NIH HHS / United States
P50 HG 002790 / HG / NHGRI NIH HHS / United States
R01 GM071966 / GM / NIGMS NIH HHS / United States
R33 HG003070 / HG / NHGRI NIH HHS / United States