ArticleGenome research2019
Mapping global and local coevolution across 600 species to identify novel homologous recombination repair genes.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 45 citations in OpenAlex.
- CladeOScope-GSA: Revealing Evolutionary Associations Across Gene Sets.International journal of molecular sciences · 2026Article
- Evolution of the Nonvisual and Visual Opsin Gene Repertoire in Ray-Finned Fishes.Genome biology and evolution · 2025Article
- EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals.Nature communications · 2025Article
- Sensitive detection of synthetic response to cancer immunotherapy driven by gene paralog pairs.Patterns (New York, N.Y.) · 2025Article
- Using multi-scale genomics to associate poorly annotated genes with rare diseases.Genome medicine · 2024Article
- Mining salt stress-related genes inaBIOTECH · 2023Article
- Mutational pattern off homologous recombination repair (HRR)-related genes in upper tract urothelial carcinoma.Cancer medicine · 2023Article
- Relationship between homologous recombination deficiency and clinical features of breast cancer based on genomic scar score.Breast (Edinburgh, Scotland) · 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
- Genetic analyses of DNA repair pathway associated genes implicate new candidate cancer predisposing genes in ancestrally defined ovarian cancer cases.Frontiers in oncology · 2023Article
- Cross-species identification of cancer resistance-associated genes that may mediate human cancer risk.Science advances · 2022Article
- Multi-omics data integration analysis identifies the spliceosome as a key regulator of DNA double-strand break repair.NAR cancer · 2022Article
- Machine-learning of complex evolutionary signals improves classification of SNVs.NAR genomics and bioinformatics · 2022Article
- Validation of a Novel Double Control Quantitative Copy Number PCR Method to Quantify Off-Target Transgene Integration after CRISPR-Induced DNA Modification.Methods and protocols · 2022Article
- Inverse Potts model improves accuracy of phylogenetic profiling.Bioinformatics (Oxford, England) · 2022Article
- Article
- Identifying protein function and functional links based on large-scale co-occurrence patterns.PloS one · 2022Article
- HRD-MILN: Accurately estimate tumor homologous recombination deficiency status from targeted panel sequencing data.Frontiers in genetics · 2022Article
- Co-evolution based machine-learning for predicting functional interactions between human genes.Nature communications · 2021Article
- Current gene panels account for nearly all homologous recombination repair-associated multiple-case breast cancer families.NPJ breast cancer · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The homologous recombination repair (HRR) pathway repairs DNA double-strand breaks in an error-free manner. Mutations in HRR genes can result in increased mutation rate and genomic rearrangements, and are associated with numerous genetic disorders and cancer. Despite intensive research, the HRR pathway is not yet fully mapped. Phylogenetic profiling analysis, which detects functional linkage between genes using coevolution, is a powerful approach to identify factors in many pathways. Nevertheless, phylogenetic profiling has limited predictive power when analyzing pathways with complex evolutionary dynamics such as the HRR. To map novel HRR genes systematically, we developed clade phylogenetic profiling (CladePP). CladePP detects local coevolution across hundreds of genomes and points to the evolutionary scale (e.g., mammals, vertebrates, animals, plants) at which coevolution occurred. We found that multiscale coevolution analysis is significantly more biologically relevant and sensitive to detect gene function. By using CladePP, we identified dozens of unrecognized genes that coevolved with the HRR pathway, either globally across all eukaryotes or locally in different clades. We validated eight genes in functional biological assays to have a role in DNA repair at both the cellular and organismal levels. These genes are expected to play a role in the HRR pathway and might lead to a better understanding of missing heredity in HRR-associated cancers (e.g., heredity breast and ovarian cancer). Our platform presents an innovative approach to predict gene function, identify novel factors related to different diseases and pathways, and characterize gene evolution.
Indexed as
Identifiers
What OpenQuestion holds
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.