ArticleGenome research2002
Inferring domain-domain interactions from protein-protein interactions.
Article in Genome research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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Who cites it
125 citing papers in PubMed, 448 citations in OpenAlex.
- Mapping of Phenotype Specific Host-Microbiome Protein-Protein Interaction Networks in Colorectal Cancer Using Deep Learning.International journal of molecular sciences · 2026Article
- Rewiring Oncogenic Transcriptional Complexes with Domain-ALTeration Chimeras (DALTACs) in Prostate Cancer.bioRxiv : the preprint server for biology · 2026Article
- Repeatability of protein structural evolution following convergent gene fusions.Nature communications · 2025Article
- Mutual annotation-based prediction of protein domain functions with Domain2GO.Protein science : a publication of the Protein Society · 2024Article
- In silico protein function prediction: the rise of machine learning-based approaches.Medical review (2021) · 2023Review
- Computational Network Inference for Bacterial Interactomics.mSystems · 2022Review
- PFP-GO: Integrating protein sequence, domain and protein-protein interaction information for protein function prediction using ranked GO terms.Frontiers in genetics · 2022Article
- PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.PLoS computational biology · 2021Article
- Study on cocoonase, sericin, and degumming of silk cocoon: computational and experimental.Journal, genetic engineering & biotechnology · 2021Article
- Predicting Protein-Protein Interactions Between Rice and Blast Fungus Using Structure-Based Approaches.Frontiers in plant science · 2021Article
- Prediction of Protein-Protein Interactions Based on Domain.Computational and mathematical methods in medicine · 2019Article
- A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks.BMC bioinformatics · 2017Article
- Cancerouspdomains: comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains.BMC bioinformatics · 2017Article
- From sequencing data to gene functions: co-functional network approaches.Animal cells and systems · 2017Review
- Enhancing interacting residue prediction with integrated contact matrix prediction in protein-protein interaction.EURASIP journal on bioinformatics & systems biology · 2016Article
- Inference of protein-protein interaction networks from multiple heterogeneous data.EURASIP journal on bioinformatics & systems biology · 2016Article
- Weighted mutual information analysis substantially improves domain-based functional network models.Bioinformatics (Oxford, England) · 2016Article
- 3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.Biophysical journal · 2016Article
- Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships.BMC systems biology · 2016Article
- A simple feature construction method for predicting upstream/downstream signal flow in human protein-protein interaction networks.Scientific reports · 2015Article
65 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
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Abstract
The interaction between proteins is one of the most important features of protein functions. Behind protein-protein interactions there are protein domains interacting physically with one another to perform the necessary functions. Therefore, understanding protein interactions at the domain level gives a global view of the protein interaction network, and possibly of protein functions. Two research groups used yeast two-hybrid assays to generate 5719 interactions between proteins of the yeast Saccharomyces cerevisiae. This allows us to study the large-scale conserved patterns of interactions between protein domains. Using evolutionarily conserved domains defined in a protein-domain database called PFAM (http://PFAM.wustl.edu), we apply a Maximum Likelihood Estimation method to infer interacting domains that are consistent with the observed protein-protein interactions. We estimate the probabilities of interactions between every pair of domains and measure the accuracies of our predictions at the protein level. Using the inferred domain-domain interactions, we predict interactions between proteins. Our predicted protein-protein interactions have a significant overlap with the protein-protein interactions (MIPS: http://mips.gfs.de) obtained by methods other than the two-hybrid assays. The mean correlation coefficient of the gene expression profiles for our predicted interaction pairs is significantly higher than that for random pairs. Our method has shown robustness in analyzing incomplete data sets and dealing with various experimental errors. We found several novel protein-protein interactions such as RPS0A interacting with APG17 and TAF40 interacting with SPT3, which are consistent with the functions of the proteins.
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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.