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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...

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Autores principales: Ghatak, Sankha, King, Zachary A, Sastry, Anand, Palsson, Bernhard O
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
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.
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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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