The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function
The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function
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DOI：
10.1093/nar/gkz030
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发表时间：
2019-03-18
影响因子：
14.9
通讯作者：
Palsson, Bernhard O.
中科院分区：
文献类型：
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作者：
Ghatak, Sankha;King, Zachary A.;Palsson, Bernhard O.
大肠杆菌K-12 MG 1655的实验研究往往牵连在细胞表型的注释不佳的基因。然而，我们对这些基因缺乏系统的了解。有多少人？他们可以获得哪些信息？它们有什么共同的特征可以解释我们理解上的差距？建立预测性的E.大肠杆菌不可避免地面临这种知识鸿沟。我们通过从EcoCyc、EcoGene、UniProt和RegulonDB的知识库中组装注释来系统地处理这些问题。我们确定了缺乏功能实验证据的基因（y-ome '），其中包括4623个独特基因中的1600个（34.6%），其中111个完全没有功能证据。另外220个基因（4.7%）是假基因或幻影基因。y-ome基因倾向于具有较低的表达水平，并且在E. coli染色体。在y-ome基因的证据中，最常见的是它们是膜蛋白和转运蛋白。我们解决了E.本文讨论了y-ome在大肠杆菌系统学改良中的价值。大肠杆菌的知识库，并将其扩展到其他生物。
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.