Gene annotation and network inference by phylogenetic profiling

BMC Bioinformatics
Jie WuCharles DeLisi

Abstract

Phylogenetic analysis is emerging as one of the most informative computational methods for the annotation of genes and identification of evolutionary modules of functionally related genes. The effectiveness with which phylogenetic profiles can be utilized to assign genes to pathways depends on an appropriate measure of correlation between gene profiles, and an effective decision rule to use the correlate. Current methods, though useful, perform at a level well below what is possible, largely because performance of the latter deteriorates rapidly as coverage increases. We introduce, test and apply a new decision rule, correlation enrichment (CE), for assigning genes to functional categories at various levels of resolution. Among the results are: (1) CE performs better than standard guilt by association (SGA, assignment to a functional category when a simple correlate exceeds a pre-specified threshold) irrespective of the number of genes assigned (i.e. coverage); improvement is greatest at high coverage where precision (positive predictive value) of CE is approximately 6-fold higher than that of SGA. (2) CE is estimated to allocate each of the 2918 unannotated orthologs to KEGG pathways with an average precision of 49% (approxima...Continue Reading

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Citations

May 8, 2007·Nature Biotechnology·Zhenjun HuCharles DeLisi
May 31, 2007·Journal of the Royal Society, Interface·Philip R KenscheMartijn A Huynen
Feb 27, 2008·BMC Bioinformatics·Bolan LinghuCharles DeLisi
May 7, 2009·Genome Biology·Tamir TullerEytan Ruppin
Jan 24, 2013·PloS One·Fotis E PsomopoulosChristos A Ouzounis
Jul 22, 2014·BMC Medical Genomics·Feng TianZhenjun Hu
Jul 7, 2009·Trends in Microbiology·James C HuDeborah A Siegele
Jul 4, 2012·Journal of Biosciences·Garima KhandelwalB Jayaram
Feb 11, 2009·Evolutionary Bioinformatics Online·Saurav Singh, Dennis P Wall

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Methods Mentioned

BETA
phylogenetic profile
phylogenetic profiles
SGA
two hybrid
Y2H
phylogenetic profiling
2-hybrid

Software Mentioned

Prolinks
SGA
VisANT
MathType
Phydbac
STRING

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