ArticlePLoS biology2009
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.
Article in PLoS biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 189 papers.
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Who cites it
189 citing papers in PubMed.
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- Large-scale protein interactome reveals lineage-specific genes driving plant-parasitic nematode adaptive innovations.Science advances · 2025Article
- Complex interplay between gene deletions and the environment uncovers cellular roles for genes of unknown function inmSystems · 2025Article
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- Exploring interspecific interaction variability in microbiota: A review.Engineering microbiology · 2024Review
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- Challenging a decades-old paradigm: ProB and ProA do not channel the unstable intermediate in proline synthesis after all.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Revisiting the y-ome of Escherichia coli.Nucleic acids research · 2024Article
- The Y-ome Conundrum: Insights into Uncharacterized Genes and Approaches for Functional Annotation.Molecular and cellular biochemistry · 2024Review
- Enhancing coevolutionary signals in protein-protein interaction prediction through clade-wise alignment integration.Scientific reports · 2024Article
- A journey into the regulatory secrets of theFrontiers in pharmacology · 2024Review
- Interaction networks of Escherichia coli replication proteins under different bacterial growth conditions.Scientific data · 2023Article
- Small molecule-mediated targeting of microRNAs for drug discovery: Experiments, computational techniques, and disease implications.European journal of medicinal chemistry · 2023Review
- Evolutionary barriers to horizontal gene transfer in macrophage-associatedEvolution letters · 2023Article
- Progress toward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization of Protein Structures and Networks In Vivo.Analytical chemistry · 2023Article
- PrePPI: A Structure Informed Proteome-wide Database of Protein-Protein Interactions.Journal of molecular biology · 2023Article
- RecF protein targeting to post-replication (daughter strand) gaps II: RecF interaction with replisomes.Nucleic acids research · 2023Article
- RecF protein targeting to postreplication (daughter strand) gaps I: DNA binding by RecF and RecFR.Nucleic acids research · 2023Article
- DeepsmirUD: Prediction of Regulatory Effects on microRNA Expression Mediated by Small Molecules Using Deep Learning.International journal of molecular sciences · 2023Article
129 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
23 authors.
Funding
Abstract
One-third of the 4,225 protein-coding genes of Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted to E. coli, including pathogenic strains. To elucidate the orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged E. coli strains and generated comprehensive genomic context inferences to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel. Clustering of the respective probabilistic networks revealed putative orphan membership in discrete multiprotein complexes and functional modules together with annotated gene products, whereas a machine-learning strategy based on network integration implicated the orphans in specific biological processes. We provide additional experimental evidence supporting orphan participation in protein synthesis, amino acid metabolism, biofilm formation, motility, and assembly of the bacterial cell envelope. This resource provides a "systems-wide" functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins.
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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.