Enhancing the prediction of protein pairings between interacting families using orthology information.

BMC Bioinformatics
José M G IzarzugazaAlfonso Valencia

Abstract

It has repeatedly been shown that interacting protein families tend to have similar phylogenetic trees. These similarities can be used to predicting the mapping between two families of interacting proteins (i.e. which proteins from one family interact with which members of the other). The correct mapping will be that which maximizes the similarity between the trees. The two families may eventually comprise orthologs and paralogs, if members of the two families are present in more than one organism. This fact can be exploited to restrict the possible mappings, simply by impeding links between proteins of different organisms. We present here an algorithm to predict the mapping between families of interacting proteins which is able to incorporate information regarding orthologues, or any other assignment of proteins to "classes" that may restrict possible mappings. For the first time in methods for predicting mappings, we have tested this new approach on a large number of interacting protein domains in order to statistically assess its performance. The method accurately predicts around 80% in the most favourable cases. We also analysed in detail the results of the method for a well defined case of interacting families, the sensor ...Continue Reading

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Citations

Mar 6, 2013·Nature Reviews. Genetics·David de JuanAlfonso Valencia
Apr 7, 2010·Bioinformatics·David Ochoa, Florencio Pazos
Mar 9, 2012·Bioinformatics·Iman HajirasoulihaS Cenk Sahinalp
Jun 17, 2010·Molecular Biology and Evolution·Simon C Lovell, David L Robertson
Aug 22, 2009·Genome Research·Elisabeth R M Tillier, Robert L Charlebois
Feb 26, 2014·BMC Bioinformatics·Mohammed El-KebirGunnar W Klau
Jun 5, 2014·Annual Review of Biophysics·Donald Petrey, Barry Honig
Nov 5, 2014·Frontiers in Cell and Developmental Biology·David Ochoa, Florencio Pazos
Dec 15, 2016·Proceedings of the National Academy of Sciences of the United States of America·Juan Rodriguez-RivasAlfonso Valencia
Oct 15, 2019·PLoS Computational Biology·Guillaume MarmierAnne-Florence Bitbol
Aug 15, 2021·Genome Biology and Evolution·Luiz Thibério RangelGregory P Fournier

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Software Mentioned

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