ArticlePLoS computational biology2017
Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.
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 16 papers.
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Who cites it
16 citing papers in PubMed, 33 citations in OpenAlex.
- DirectContacts2: a wiring diagram of human physical protein interactions.Nature communications · 2026Article
- A cross-vertebrate brain protein interaction map identifies conserved neural and non-neural complexes.Cell reports · 2026Article
- VerteBrain reveals novel neural and non-neural protein assemblies conserved across vertebrate evolution.bioRxiv : the preprint server for biology · 2025Article
- I'm Walking into Spiderwebs: Making Sense of Protein-Protein Interaction Data.Journal of proteome research · 2024Review
- Progression of monoclonal gammopathy of undetermined significance to multiple myeloma is associated with enhanced translational quality control and overall loss of surface antigens.Journal of translational medicine · 2024Article
- Identification of Protein Complexes by Integrating Protein Abundance and Interaction Features Using a Deep Learning Strategy.International journal of molecular sciences · 2023Article
- A co-fractionation mass spectrometry-based prediction of protein complex assemblies in the developing rice aleurone-subaleurone.The Plant cell · 2021Article
- Integration of Proteomics and Other Omics Data.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Protein Complexes Form a Basis for Complex Hybrid Incompatibility.Frontiers in genetics · 2021Review
- Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold StandardMolecular & cellular proteomics : MCP · 2020Article
- Dynamic rewiring of the human interactome by interferon signaling.Genome biology · 2020Article
- Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes.Cell reports · 2019Article
- A Computational Framework for Predicting Direct Contacts and Substructures within Protein Complexes.Biomolecules · 2019Article
- Microbial Networks in SPRING - Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data.Frontiers in genetics · 2019Article
- Classification of Single Particles from Human Cell Extract Reveals Distinct Structures.Cell reports · 2018Article
- Network approaches and applications in biology.PLoS computational biology · 2017Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Determining the three dimensional arrangement of proteins in a complex is highly beneficial for uncovering mechanistic function and interpreting genetic variation in coding genes comprising protein complexes. There are several methods for determining co-complex interactions between proteins, among them co-fractionation / mass spectrometry (CF-MS), but it remains difficult to identify directly contacting subunits within a multi-protein complex. Correlation analysis of CF-MS profiles shows promise in detecting protein complexes as a whole but is limited in its ability to infer direct physical contacts among proteins in sub-complexes. To identify direct protein-protein contacts within human protein complexes we learn a sparse conditional dependency graph from approximately 3,000 CF-MS experiments on human cell lines. We show substantial performance gains in estimating direct interactions compared to correlation analysis on a benchmark of large protein complexes with solved three-dimensional structures. We demonstrate the method's value in determining the three dimensional arrangement of proteins by making predictions for complexes without known structure (the exocyst and tRNA multi-synthetase complex) and by establishing evidence for the structural position of a recently discovered component of the core human EKC/KEOPS complex, GON7/C14ORF142, providing a more complete 3D model of the complex. Direct contact prediction provides easily calculable additional structural information for large-scale protein complex mapping studies and should be broadly applicable across organisms as more CF-MS datasets become available.
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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.