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

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...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:NAR Genomics and Bioinformatics 2021-06, Vol.3 (2), p.lqab024-lqab024
Hauptverfasser: Tsaban, Tomer, Stupp, Doron, Sherill-Rofe, Dana, Bloch, Idit, Sharon, Elad, Schueler-Furman, Ora, Wiener, Reuven, Tabach, Yuval
Format: Artikel
Sprache:eng
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung: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.
ISSN:2631-9268
2631-9268
DOI:10.1093/nargab/lqab024