Phylogeny-guided interaction mapping in seven eukaryotes.

BMC Bioinformatics
Janusz Dutkowski, Jerzy Tiuryn

Abstract

The assembly of reliable and complete protein-protein interaction (PPI) maps remains one of the significant challenges in systems biology. Computational methods which integrate and prioritize interaction data can greatly aid in approaching this goal. We developed a Bayesian inference framework which uses phylogenetic relationships to guide the integration of PPI evidence across multiple datasets and species, providing more accurate predictions. We apply our framework to reconcile seven eukaryotic interactomes: H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. cerevisiae and A. thaliana. Comprehensive GO-based quality assessment indicates a 5% to 44% score increase in predicted interactomes compared to the input data. Further support is provided by gold-standard MIPS, CYC2008 and HPRD datasets. We demonstrate the ability to recover known PPIs in well-characterized yeast and human complexes (26S proteasome, endosome and exosome) and suggest possible new partners interacting with the putative SWI/SNF chromatin remodeling complex in A. thaliana. Our phylogeny-guided approach compares favorably to two standard methods for mapping PPIs across species. Detailed analysis of predictions in selected functional modul...Continue Reading

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Citations

Aug 13, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Janusz Dutkowski, Jerzy Tiuryn
Sep 11, 2012·Bioinformatics·Sèverine BérardEric Tannier
Sep 11, 2012·Bioinformatics·Ofir CohenTal Pupko
Jun 12, 2013·Nucleic Acids Research·Ofir CohenTal Pupko
Oct 3, 2012·PLoS Computational Biology·Anna C F LewisCharlotte M Deane
Mar 19, 2014·BMC Research Notes·Oussema SouiaiAlia Benkahla
Jan 24, 2017·IEEE Transactions on Nanobioscience·Min YeBernard M E Moret
Jun 22, 2018·Current Protocols in Protein Science·Ziyun Ding, Daisuke Kihara
Jun 21, 2019·Scientific Reports·Ziyun Ding, Daisuke Kihara

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Methods Mentioned

BETA
two-hybrid
Y2H
phylogenetic profiles
phylogenetic profile
interaction prediction
interaction predictions

Software Mentioned

Cytoscape
Integ
3sp
CAPPI
SemSim R
Pred
Interlog
All
InteroPORC

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