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The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function
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 ou...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6412132/ https://www.ncbi.nlm.nih.gov/pubmed/30698741 http://dx.doi.org/10.1093/nar/gkz030 |
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author | Ghatak, Sankha King, Zachary A Sastry, Anand Palsson, Bernhard O |
author_facet | Ghatak, Sankha King, Zachary A Sastry, Anand Palsson, Bernhard O |
author_sort | Ghatak, Sankha |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6412132 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-64121322019-03-18 The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function Ghatak, Sankha King, Zachary A Sastry, Anand Palsson, Bernhard O Nucleic Acids Res Genomics 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. Oxford University Press 2019-03-18 2019-01-30 /pmc/articles/PMC6412132/ /pubmed/30698741 http://dx.doi.org/10.1093/nar/gkz030 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Genomics Ghatak, Sankha King, Zachary A Sastry, Anand Palsson, Bernhard O The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function |
title | The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function |
title_full | The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function |
title_fullStr | The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function |
title_full_unstemmed | The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function |
title_short | The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function |
title_sort | y-ome defines the 35% of escherichia coli genes that lack experimental evidence of function |
topic | Genomics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6412132/ https://www.ncbi.nlm.nih.gov/pubmed/30698741 http://dx.doi.org/10.1093/nar/gkz030 |
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