Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.
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DOI：
10.1093/bib/bbr042
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发表时间：
2011-09
影响因子：
9.5
通讯作者：
Thomas PD
中科院分区：
文献类型：
--
作者：
Gaudet P;Livstone MS;Lewis SE;Thomas PD
基因本体论（GO）项目的目标是提供一种统一的方法来描述来自所有生命王国的生物体的基因产物的功能，从而实现对基因组数据的分析。蛋白质注释要么基于实验，要么从蛋白质序列预测。由于大多数序列尚未通过实验表征，因此大多数可用的注释需要基于预测。为了尽可能准确地进行推断，GO联盟的参考基因组计划正在使用一个明确的进化框架，以半自动化的方式从实验注释中推断来自广泛基因组的蛋白质注释。管道中的大多数组件，如选择序列，构建多序列比对和系统发育树，检索实验注释和存放推断注释，都是完全自动化的。然而，我们管道中最关键的一步依赖于生物学家专家的软件辅助管理。这个策展工具，系统发育注释和推理工具（PAINT），帮助策展人推断蛋白质家族成员之间的注释。PAINT允许策展人对进化过程中功能的获得和丧失做出精确的断言，并记录这些断言的证据（例如实验支持的GO注释和系统发育信息，包括正字法）。在这篇文章中，我们描述了我们如何使用PAINT推断蛋白质功能的系统发育背景下，强调其优势，局限性和指导方针。我们还讨论了具体的例子，显示PAINT注释与其他高度使用的同源性为基础的方法产生的比较。
The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data. Protein annotations are either based on experiments or predicted from protein sequences. Since most sequences have not been experimentally characterized, most available annotations need to be based on predictions. To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental annotations in a semi-automated manner. Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are fully automated. However, the most crucial step in our pipeline relies on software-assisted curation by an expert biologist. This curation tool, Phylogenetic Annotation and INference Tool (PAINT) helps curators to infer annotations among members of a protein family. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions. In this article, we describe how we use PAINT to infer protein function in a phylogenetic context with emphasis on its strengths, limitations and guidelines. We also discuss specific examples showing how PAINT annotations compare with those generated by other highly used homology-based methods.
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影响因子：
4.3
作者：
Reference Genome Group of the Gene Ontology Consortium
通讯作者：
Reference Genome Group of the Gene Ontology Consortium
影响因子：
7
作者：
Vilella, Albert J.;Severin, Jessica;Birney, Ewan
通讯作者：
Birney, Ewan
影响因子：
4.3
作者：
Engelhardt BE;Jordan MI;Muratore KE;Brenner SE
通讯作者：
Brenner SE
影响因子：
14.9
作者：
Eisen, JA
通讯作者：
Eisen, JA
影响因子：
3
作者：
Deegan (nee Clark), Jennifer I.;Dimmer, Emily C.;Mungall, Christopher J.
通讯作者：
Mungall, Christopher J.