ArticlePLoS computational biology2011
Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Rummagene: massive mining of gene sets from supporting materials of biomedical research publications.Communications biology · 2024Article
- Network inference from perturbation time course data.NPJ systems biology and applications · 2022Article
- Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.PLoS computational biology · 2017Article
- Article
- Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction.Computational biology and chemistry · 2015Article
- Cluster-based assessment of protein-protein interaction confidence.BMC bioinformatics · 2012Article
- Sets2Networks: network inference from repeated observations of sets.BMC systems biology · 2012Article
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Authors and funding
12 authors.
Funding
Abstract
Coregulator proteins (CoRegs) are part of multi-protein complexes that transiently assemble with transcription factors and chromatin modifiers to regulate gene expression. In this study we analyzed data from 3,290 immuno-precipitations (IP) followed by mass spectrometry (MS) applied to human cell lines aimed at identifying CoRegs complexes. Using the semi-quantitative spectral counts, we scored binary protein-protein and domain-domain associations with several equations. Unlike previous applications, our methods scored prey-prey protein-protein interactions regardless of the baits used. We also predicted domain-domain interactions underlying predicted protein-protein interactions. The quality of predicted protein-protein and domain-domain interactions was evaluated using known binary interactions from the literature, whereas one protein-protein interaction, between STRN and CTTNBP2NL, was validated experimentally; and one domain-domain interaction, between the HEAT domain of PPP2R1A and the Pkinase domain of STK25, was validated using molecular docking simulations. The scoring schemes presented here recovered known, and predicted many new, complexes, protein-protein, and domain-domain interactions. The networks that resulted from the predictions are provided as a web-based interactive application at http://maayanlab.net/HT-IP-MS-2-PPI-DDI/.
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