ArticleNucleic acids research2024
Revisiting the y-ome of Escherichia coli.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Proteome Remodeling of a Carbapenem-Resistant Escherichia coli Strain upon Meropenem Exposure.Journal of proteome research · 2026Article
- Selective Reprogramming of Ribosome Assembly and Translational Control during Bacterial Growth Phase Transitions.ACS omega · 2026Article
- The microbial unknome, a repertoire for microbial chatting?Heredity · 2026Review
- Comparative analysis of gene importance inmSystems · 2026Article
- Uncovering resistance pathways to first- and last-line antibiotics inMicrobial genomics · 2026Article
- Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis.Genome medicine · 2026Article
- Predictive modeling of gene expression and localization of DNA binding site using deep convolutional neural networks.PLoS computational biology · 2026Article
- PyamilySeq: exposing the fragility of conventional gene (re)clustering and prokaryotic pangenomic inference methods.NAR genomics and bioinformatics · 2026Article
- Human body temperature cues widespread changes in virulence gene expression in uropathogenicInfection and immunity · 2026Article
- Transcriptomic profiling of a commensal Escherichia coli lysogen in simulated intestinal fluid reveals broad changes in both core and accessory regions of the genome.BMC genomics · 2026Article
- Microgravity-induced constraints on melanin bioproduction: investigating E. coli metabolic responses aboard the international space station.NPJ microgravity · 2026Article
- The transcriptional regulatory network of the Escherichia coli MG1655 reference strain.Nucleic acids research · 2026Article
- The uncharacterizedmicroPublication biology · 2026Article
- The Algorithm for Reversible Jump Inference of Motifs.bioRxiv : the preprint server for biology · 2025Article
- The EcoCyc database (2025).EcoSal Plus · 2025Review
- Global Transcriptomic Profiling Reveals Conserved and Phage-specific Responses to Phage Infection in Escherichia Coli.Microbial ecology · 2025Article
- Carrot and stick: how RNase R contributes to function and destruction of the translation machinery.RNA biology · 2025Review
- Asymmetric interactions and feast-famine cycles drive chaos in microbial populations.Research square · 2025Article
- Credible inferences in microbiome research: ensuring rigour, reproducibility and relevance in the era of AI.Nature reviews. Gastroenterology & hepatology · 2025Review
- Metatranscriptomics-based metabolic modeling of patient-specific urinary microbiome during infection.NPJ biofilms and microbiomes · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The model organism Escherichia coli K-12 has one of the most extensively annotated genomes in terms of functional characterization, yet a significant number of genes, ∼35%, are still considered poorly characterized. Initially genes without known functional understanding were given 'y' gene names. However, due to inconsistency in changing 'y' names to non-'y' names over the years, gene name alone does not provide sufficient information as to the characterization level of genes. Attempts to characterize y-ome genes, i.e. those that lack experimental evidence for function, are ongoing, and recent categorization based on the level of experimental evidence has helped clarify those genes that are well characterized versus uncharacterized. EcoCyc, the most comprehensive, curated genome database for E. coli K-12 substr. MG1655, has updated this approach by expanding the categories to include Partially characterized genes using a set of computational rules that includes keywords, experimental evidence codes and Gene Ontology terms. Approximately half of the previously categorized y-ome genes are now categorized as Partially characterized, leaving 15.5% (738) as Uncharacterized genes in EcoCyc. This new categorization scheme is searchable in the EcoCyc database, will be updated as new experimental evidence is curated and provides important information for research decisions.
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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.