ArticleGenome research2006
Systematic identification of functional orthologs based on protein network comparison.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed.
- Molecular mechanisms underlying early functional divergence in snake venom inferred from the genomes of two pitviper lineages.BMC biology · 2025Article
- Unveiling the functional fate of duplicated genes through expression profiling and structural analysis.Genome research · 2025Article
- For Someone, You Are the Whole World: Host-Specificity ofInternational journal of molecular sciences · 2023Article
- Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses.The plant genome · 2022Article
- Empirically classifying network mechanisms.Scientific reports · 2021Article
- Pairwise Biological Network Alignment Based on Discrete Bat Algorithm.Computational and mathematical methods in medicine · 2021Article
- Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs.PLoS biology · 2020Article
- Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals.BMC genomics · 2020Article
- Primary orthologs from local sequence context.BMC bioinformatics · 2020Article
- Pharmacological convergence reveals a lipid pathway that regulates C. elegans lifespan.Nature chemical biology · 2019Article
- A genome-scale metabolic network alignment method within a hypergraph-based framework using a rotational tensor-vector product.Scientific reports · 2018Article
- Discovering large conserved functional components in global network alignment by graph matching.BMC genomics · 2018Article
- Unified Alignment of Protein-Protein Interaction Networks.Scientific reports · 2017Article
- In-silico screening, identification and validation of a novel vaccine candidate in the fight against Plasmodium falciparum.Parasitology research · 2017Article
- Expression Pattern Similarities Support the Prediction of Orthologs Retaining Common Functions after Gene Duplication Events.Plant physiology · 2016Article
- Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions.Cold Spring Harbor protocols · 2016Article
- LK6/Mnk2a is a new kinase of alpha synuclein phosphorylation mediating neurodegeneration.Scientific reports · 2015Article
- L-GRAAL: Lagrangian graphlet-based network aligner.Bioinformatics (Oxford, England) · 2015Article
- Algorithmic approaches to protein-protein interaction site prediction.Algorithms for molecular biology : AMB · 2015Article
- Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments.BMC systems biology · 2015Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Annotating protein function across species is an important task that is often complicated by the presence of large paralogous gene families. Here, we report a novel strategy for identifying functionally related proteins that supplements sequence-based comparisons with information on conserved protein-protein interactions. First, the protein interaction networks of two species are aligned by assigning proteins to sequence homology clusters using the Inparanoid algorithm. Next, probabilistic inference is performed on the aligned networks to identify pairs of proteins, one from each species, that are likely to retain the same function based on conservation of their interacting partners. Applying this method to Drosophila melanogaster and Saccharomyces cerevisiae, we analyze 121 cases for which functional orthology assignment is ambiguous when sequence similarity is used alone. In 61 of these cases, the network supports a different protein pair than that favored by sequence comparisons. These results suggest that network analysis can be used to provide a key source of information for refining sequence-based homology searches.
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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.