CladeOScope: Functional interactions through the prism of clade-wise co-evolution

Tomer Tsaban, Doron Stupp, Dana Sherill-Rofe, Idit Bloch, Elad Sharon, Ora Schueler-Furman, Reuven Wiener, Yuval Tabach*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

Abstract

Mapping co-evolved genes via phylogenetic profiling (PP) is a powerful approach to uncover functional interactions between genes and to associate them with pathways. Despite many successful endeavors, the understanding of co-evolutionary signals in eukaryotes remains partial. Our hypothesis is that 'Clades', branches of the tree of life (e.g. primates and mammals), encompass signals that cannot be detected by PP using all eukaryotes. As such, integrating information from different clades should reveal local co-evolution signals and improve function prediction. Accordingly, we analyzed 1028 genomes in 66 clades and demonstrated that the co-evolutionary signal was scattered across clades. We showed that functionally related genes are frequently co-evolved in only parts of the eukaryotic tree and that clades are complementary in detecting functional interactions within pathways. We examined the non-homologous end joining pathway and the UFM1 ubiquitin-like protein pathway and showed that both demonstrated distinguished co-evolution patterns in specific clades. Our research offers a different way to look at co-evolution across eukaryotes and points to the importance of modular co-evolution analysis. We developed the 'CladeOScope' PP method to integrate information from 16 clades across over 1000 eukaryotic genomes and is accessible via an easy to use web server at http://cladeoscope.cs.huji.ac.il.

Original languageAmerican English
Article numberlqab024
JournalNAR Genomics and Bioinformatics
Volume3
Issue number2
DOIs
StatePublished - 1 Jun 2021

Bibliographical note

Publisher Copyright:
© 2021 The Author(s) 2021. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.

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