ArticleBMC genomics2009
Identification of mammalian orthologs using local synteny.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 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
35 citing papers in PubMed, 87 citations in OpenAlex.
- Quantifying the Influence of Genetic Context on Duplicated Mammalian Genes.Molecular biology and evolution · 2026Article
- Quantifying the influence of genetic context on duplicated mammalian genes.bioRxiv : the preprint server for biology · 2025Article
- Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX.Nature protocols · 2024Review
- OrthoRefine: automated enhancement of prior ortholog identification via synteny.BMC bioinformatics · 2024Article
- Integrating gene annotation with orthology inference at scale.Science (New York, N.Y.) · 2023Article
- HGD: an integrated homologous gene database across multiple species.Nucleic acids research · 2023Article
- Automated annotation of human centromeres with HORmon.Genome research · 2022Article
- Phenolic degradation by catechol dioxygenases is associated with pathogenic fungi with a necrotrophic lifestyle in the Ceratocystidaceae.G3 (Bethesda, Md.) · 2022Article
- Manual annotation ofF1000Research · 2022Article
- Identification and Expression Profiling of Toll-Like Receptors of Brown Trout (International journal of molecular sciences · 2020Article
- Primary orthologs from local sequence context.BMC bioinformatics · 2020Article
- Genome-wide comparative analysis of the BAHD superfamily in seven Rosaceae species and expression analysis in pear (Pyrus bretschneideri).BMC plant biology · 2020Article
- Bioinformatics Screening of Genes Specific for Well-Regenerating Vertebrates Reveals c-answer, a Regulator of Brain Development and Regeneration.Cell reports · 2019Article
- OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation.Genomics, proteomics & bioinformatics · 2017Article
- Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses.Scientific reports · 2017Article
- GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm.BMC evolutionary biology · 2016Article
- Saprophytic and pathogenic fungi in the Ceratocystidaceae differ in their ability to metabolize plant-derived sucrose.BMC evolutionary biology · 2015Article
- OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy.Genome biology · 2015Article
- An event-driven approach for studying gene block evolution in bacteria.Bioinformatics (Oxford, England) · 2015Article
- Genome-wide identification and comparative analysis of the heat shock transcription factor family in Chinese white pear (Pyrus bretschneideri) and five other Rosaceae species.BMC plant biology · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAccurate determination of orthology is central to comparative genomics. For vertebrates in particular, very large gene families, high rates of gene duplication and loss, multiple mechanisms of gene duplication, and high rates of retrotransposition all combine to make inference of orthology between genes difficult. Many methods have been developed to identify orthologous genes, mostly based upon analysis of the inferred protein sequence of the genes. More recently, methods have been proposed that use genomic context in addition to protein sequence to improve orthology assignment in vertebrates. Such methods have been most successfully implemented in fungal genomes and have long been used in prokaryotic genomes, where gene order is far less variable than in vertebrates. However, to our knowledge, no explicit comparison of synteny and sequence based definitions of orthology has been reported in vertebrates, or, more specifically, in mammals.
resultsWe test a simple method for the measurement and utilization of gene order (local synteny) in the identification of mammalian orthologs by investigating the agreement between coding sequence based orthology (Inparanoid) and local synteny based orthology. In the 5 mammalian genomes studied, 93% of the sampled inter-species pairs were found to be concordant between the two orthology methods, illustrating that local synteny is a robust substitute to coding sequence for identifying orthologs. However, 7% of pairs were found to be discordant between local synteny and Inparanoid. These cases of discordance result from evolutionary events including retrotransposition and genome rearrangements.
conclusionsBy analyzing cases of discordance between local synteny and Inparanoid we show that local synteny can distinguish between true orthologs and recent retrogenes, can resolve ambiguous many-to-many orthology relationships into one-to-one ortholog pairs, and might be used to identify cases of non-orthologous gene displacement by retroduplicated paralogs.
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.