ArticleBMC bioinformatics2005
Computational verification of protein-protein interactions by orthologous co-expression.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 29 citations in OpenAlex.
- Computational insights in CD58 binding to ASFV CD2v and in silico optimization of nanobody designs against the interface.Open veterinary journal · 2025Article
- Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context.Frontiers in molecular biosciences · 2022Review
- Probability weighted ensemble transfer learning for predicting interactions between HIV-1 and human proteins.PloS one · 2013Article
- Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system.Microbiology and molecular biology reviews : MMBR · 2012Review
- HAPPI: an online database of comprehensive human annotated and predicted protein interactions.BMC genomics · 2009Article
- Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression.BMC genomics · 2009Article
- Co-expression among constituents of a motif in the protein-protein interaction network.Journal of bioinformatics and computational biology · 2009Article
- Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis.BMC bioinformatics · 2009Article
- Identification of semaphorin 5A interacting protein by applying apriori knowledge and peptide complementarity related to protein evolution and structure.Genomics, proteomics & bioinformatics · 2008Article
- Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis.PLoS computational biology · 2008Article
- Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment.BMC bioinformatics · 2007Article
- Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions.Journal of molecular biology · 2006Article
- Protein-protein interactions more conserved within species than across species.PLoS computational biology · 2006Article
- Protein complex compositions predicted by structural similarity.Nucleic acids research · 2006Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
backgroundHigh-throughput methods identify an overwhelming number of protein-protein interactions. However, the limited accuracy of these methods results in the false identification of many spurious interactions. Accordingly, the resulting interactions are regarded as hypothetical and computational methods are needed to increase their confidence. Several methods have recently been suggested for this purpose including co-expression as a confidence measure for interacting proteins, but their performance is still quite poor.
resultsWe introduce a novel computational method for verification of protein-protein interactions based on the co-expression of orthologs of interacting partners. The performance of our method is analysed using known S. cerevisiae interactions, and is shown to overcome limitations of previous methods. We present specific examples of known and putative interactions that are detected by our method and not by previous methods, and suggest that they represent transient interactions that might have been conserved and stabilized in other species.
conclusionCo-expression of orthologous protein-pairs can be used to increase the confidence of hypothetical protein-protein interactions in S. cerevisiae as well as in other species. This approach may be especially useful for species with no available expression profiles and for transient interactions.
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