ArticlePLoS computational biology2017
Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Alternative splicing fine-tunes modular protein interfaces to control protein localization.Nature structural & molecular biology · 2026Article
- DeepISO: deep learning-powered prediction of protein-protein interaction rewiring generated by alternative splicing.Genome biology · 2026Article
- Predicting interaction-specific protein-protein interaction perturbations by missense variants with MutPred-PPI.bioRxiv : the preprint server for biology · 2026Article
- The power and limits of predicting inter-protein exon-exon interactions using protein 3D structures.Bioinformatics advances · 2026Article
- PPIXpress and PPICompare webservers infer condition-specific and differential PPI networks.Bioinformatics advances · 2025Article
- Signals in the Cells: Multimodal and Contextualized Machine Learning Foundations for Therapeutics.bioRxiv : the preprint server for biology · 2024Article
- Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart.Journal of proteome research · 2024Article
- N-terminal proteoforms may engage in different protein complexes.Life science alliance · 2023Article
- Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease.Human molecular genetics · 2022Review
- EventPointer 3.0: flexible and accurate splicing analysis that includes studying the differential usage of protein-domains.NAR genomics and bioinformatics · 2022Article
- Are transient protein-protein interactions more dispensable?PLoS computational biology · 2022Article
- The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells.Science (New York, N.Y.) · 2022Article
- FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks.NAR genomics and bioinformatics · 2021Article
- DIGGER: exploring the functional role of alternative splicing in protein interactions.Nucleic acids research · 2021Article
- Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data.Frontiers in bioinformatics · 2021Review
- Mutation Edgotype Drives Fitness Effect in Human.Frontiers in bioinformatics · 2021Article
- An analysis of tissue-specific alternative splicing at the protein level.PLoS computational biology · 2020Article
- Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction.Current genomics · 2020Review
- Edgetic perturbation signatures represent known and novel cancer biomarkers.Scientific reports · 2020Article
- ISOGO: Functional annotation of protein-coding splice variants.Scientific reports · 2020Article
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Authors and funding
4 authors.
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Abstract
Alternative splicing is known to remodel protein-protein interaction networks ("interactomes"), yet large-scale determination of isoform-specific interactions remains challenging. We present a domain-based method to predict the isoform interactome from the reference interactome. First, we construct the domain-resolved reference interactome by mapping known domain-domain interactions onto experimentally-determined interactions between reference proteins. Then, we construct the isoform interactome by predicting that an isoform loses an interaction if it loses the domain mediating the interaction. Our prediction framework is of high-quality when assessed by experimental data. The predicted human isoform interactome reveals extensive network remodeling by alternative splicing. Protein pairs interacting with different isoforms of the same gene tend to be more divergent in biological function, tissue expression, and disease phenotype than protein pairs interacting with the same isoforms. Our prediction method complements experimental efforts, and demonstrates that integrating structural domain information with interactomes provides insights into the functional impact of alternative splicing.
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