ArticleBMC genomics2018
Context-specific interactions in literature-curated protein interaction databases.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry.Nature communications · 2023Pooled it
- Strategies for constructing context-specific protein-protein interaction networks.Briefings in bioinformatics · 2026Review
- Temporal network analysis in systems biology: concepts, inference, and validation.Frontiers in bioinformatics · 2026Review
- Sequestration of ribosome biogenesis factors in HSV-1 nuclear aggregates revealed by spatially resolved thermal profiling.Science advances · 2025Article
- Modulation of TvRAD51 Recombinase inPathogens (Basel, Switzerland) · 2025Article
- Psychiatric Genomics 2025: State of the Art and the Path Forward.The Psychiatric clinics of North America · 2025Review
- Tapioca: a platform for predicting de novo protein-protein interactions in dynamic contexts.Nature methods · 2024Article
- Software and Databases for Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets.BMC bioinformatics · 2022Article
- Recent progress in mass spectrometry-based strategies for elucidating protein-protein interactions.Cellular and molecular life sciences : CMLS · 2021Review
- Article
- Contextualized Protein-Protein Interactions.Patterns (New York, N.Y.) · 2021Article
- On the Robustness of Graph-Based Clustering to Random Network Alterations.Molecular & cellular proteomics : MCP · 2021Article
- Mapping, Structure and Modulation of PPI.Frontiers in chemistry · 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
- Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks.Molecular & cellular proteomics : MCP · 2020Review
- Profiling theeLife · 2019Article
- Mass Spectrometry-Based Proteomics Technologies to Define Endogenous Protein-Protein Interactions and Their Applications to Cancer and Viral Infectious Diseases.Mass spectrometry reviewsReview
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundDatabases of literature-curated protein-protein interactions (PPIs) are often used to interpret high-throughput interactome mapping studies and estimate error rates. These databases combine interactions across thousands of published studies and experimental techniques. Because the tendency for two proteins to interact depends on the local conditions, this heterogeneity of conditions means that only a subset of database PPIs are interacting during any given experiment. A typical use of these databases as gold standards in interactome mapping projects, however, assumes that PPIs included in the database are indeed interacting under the experimental conditions of the study.
resultsUsing raw data from 20 co-fractionation experiments and six published interactomes, we demonstrate that this assumption is often false, with up to 55% of purported gold standard interactions showing no evidence of interaction, on average. We identify a subset of CORUM database complexes that do show consistent evidence of interaction in co-fractionation studies, and we use this subset as gold standards to dramatically improve interactome mapping as judged by the number of predicted interactions at a given error rate.
conclusionsWe recommend using this CORUM subset as the gold standard set in future co-fractionation studies. More generally, we recommend using the subset of literature-curated PPIs that are specific to the experimental context whenever possible.
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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.