ArticleNucleic acids research2019
The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
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94 citing papers in PubMed.
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- The microbial unknome, a repertoire for microbial chatting?Heredity · 2026Review
- Intracellular microbial shifts during COVID-19 infection and longitudinal recovery revealed by single-cell RNA sequencing.iScience · 2026Article
- A systems-level atlas of carbon-response transcriptional states inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Systematic design of auxotrophic strains and media conditions to probe metabolic functions in E. coli.PLoS computational biology · 2026Article
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- Gene-level analysis of core carbohydrate metabolism across the Enterobacteriaceae pan-genome.Communications biology · 2025Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- Complex interplay between gene deletions and the environment uncovers cellular roles for genes of unknown function inmSystems · 2025Article
- Cellular function of the GndA microprotein during heat shock.bioRxiv : the preprint server for biology · 2025Article
- DeepMolecules: a web server for predicting enzyme and transporter-small molecule interactions.Nucleic acids research · 2025Article
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- Functional profiling of the sequence stockpile: a protein pair-based assessment of in silico prediction tools.Bioinformatics (Oxford, England) · 2025Article
34 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Experimental studies of Escherichia coli K-12 MG1655 often implicate poorly annotated genes in cellular phenotypes. However, we lack a systematic understanding of these genes. How many are there? What information is available for them? And what features do they share that could explain the gap in our understanding? Efforts to build predictive, whole-cell models of E. coli inevitably face this knowledge gap. We approached these questions systematically by assembling annotations from the knowledge bases EcoCyc, EcoGene, UniProt and RegulonDB. We identified the genes that lack experimental evidence of function (the 'y-ome') which include 1600 of 4623 unique genes (34.6%), of which 111 have absolutely no evidence of function. An additional 220 genes (4.7%) are pseudogenes or phantom genes. y-ome genes tend to have lower expression levels and are enriched in the termination region of the E. coli chromosome. Where evidence is available for y-ome genes, it most often points to them being membrane proteins and transporters. We resolve the misconception that a gene in E. coli whose primary name starts with 'y' is unannotated, and we discuss the value of the y-ome for systematic improvement of E. coli knowledge bases and its extension to other organisms.
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