ArticleNAR genomics and bioinformatics2021
CladeOScope: functional interactions through the prism of clade-wise co-evolution.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 28 citations in OpenAlex.
- Tubulin autoregulation mediator TTC5 regulates neuronal morphology and migration.bioRxiv : the preprint server for biology · 2026Article
- CladeOScope-GSA: Revealing Evolutionary Associations Across Gene Sets.International journal of molecular sciences · 2026Article
- C17orf75 (Njmu-R1) promotes hepatocellular carcinoma progression: a pan-cancer analysis and experimental validation.Frontiers in immunology · 2026Article
- Article
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- C11orf54 catalyzes L-xylulose formation in human metabolism.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Predicting Protein Function in the AI and Big Data Era.Biochemistry · 2025Review
- Using multi-scale genomics to associate poorly annotated genes with rare diseases.Genome medicine · 2024Article
- A genome-wide screen reveals new regulators of the 2-cell-like cell state.Nature structural & molecular biology · 2023Article
- Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy.The EMBO journal · 2023Article
- RPL26/uL24 UFMylation is essential for ribosome-associated quality control at the endoplasmic reticulum.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- RPL26/uL24 UFMylation is essential for ribosome-associated quality control at the endoplasmic reticulum.bioRxiv : the preprint server for biology · 2023Article
- Systematic proximal mapping of the classical RAD51 paralogs unravel functionally and clinically relevant interactors for genome stability.PLoS genetics · 2022Article
- Cross-species identification of cancer resistance-associated genes that may mediate human cancer risk.Science advances · 2022Article
- Machine-learning of complex evolutionary signals improves classification of SNVs.NAR genomics and bioinformatics · 2022Article
- Multi-omics data integration analysis identifies the spliceosome as a key regulator of DNA double-strand break repair.NAR cancer · 2022Article
- Inverse Potts model improves accuracy of phylogenetic profiling.Bioinformatics (Oxford, England) · 2022Article
- Co-evolution based machine-learning for predicting functional interactions between human genes.Nature communications · 2021Article
- Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.