ArticleBMC bioinformatics2007
A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 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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Who cites it
110 citing papers in PubMed, 1 synthesis or guideline pooled it, 281 citations in OpenAlex.
- Meta-analysis of dispensable essential genes and their interactions with bypass suppressors.Life science alliance · 2024Pooled it
- DirectContacts2: a wiring diagram of human physical protein interactions.Nature communications · 2026Article
- A protein network refinement method based on module discovery and biological information.BMC bioinformatics · 2024Article
- From beer to breadboards: yeast as a force for biological innovation.Genome biology · 2024Review
- An application of node and edge nonlinear hypergraph centrality to a protein complex hypernetwork.PloS one · 2024Article
- The protein interactome of the citrus Huanglongbing pathogen Candidatus Liberibacter asiaticus.Nature communications · 2023Article
- HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes.Genomics, proteomics & bioinformatics · 2023Article
- Recovering false negatives in CRISPR fitness screens with JLOE.Nucleic acids research · 2023Article
- Article
- Integration of probabilistic functional networks without an external Gold Standard.BMC bioinformatics · 2022Article
- Computational Network Inference for Bacterial Interactomics.mSystems · 2022Review
- An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information.BMC bioinformatics · 2021Article
- A novel essential protein identification method based on PPI networks and gene expression data.BMC bioinformatics · 2021Article
- hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies.Molecular systems biology · 2021Article
- Protein Complexes Form a Basis for Complex Hybrid Incompatibility.Frontiers in genetics · 2021Review
- Multiplex enCas12a screens detect functional buffering among paralogs otherwise masked in monogenic Cas9 knockout screens.Genome biology · 2020Article
- Article
- A network analysis revealed the essential and common downstream proteins related to inguinal hernia.PloS one · 2020Article
- Paralog buffering contributes to the variable essentiality of genes in cancer cell lines.PLoS genetics · 2019Article
- Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2019Article
50 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIdentifying all protein complexes in an organism is a major goal of systems biology. In the past 18 months, the results of two genome-scale tandem affinity purification-mass spectrometry (TAP-MS) assays in yeast have been published, along with corresponding complex maps. For most complexes, the published data sets were surprisingly uncorrelated. It is therefore useful to consider the raw data from each study and generate an accurate complex map from a high-confidence data set that integrates the results of these and earlier assays.
resultsUsing an unsupervised probabilistic scoring scheme, we assigned a confidence score to each interaction in the matrix-model interpretation of the large-scale yeast mass-spectrometry data sets. The scoring metric proved more accurate than the filtering schemes used in the original data sets. We then took a high-confidence subset of these interactions and derived a set of complexes using MCL. The complexes show high correlation with existing annotations. Hierarchical organization of some protein complexes is evident from inter-complex interactions.
conclusionWe demonstrate that our scoring method can generate an integrated high-confidence subset of observed matrix-model interactions, which we subsequently used to derive an accurate map of yeast complexes. Our results indicate that essentiality is a product of the protein complex rather than the individual protein, and that we have achieved near saturation of the yeast high-abundance, rich-media-expressed "complex-ome."
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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.