neXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects
neXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects
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DOI：
10.1021/pr300830v
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发表时间：
2013-01-01
影响因子：
4.4
通讯作者：
Lane, Lydie
中科院分区：
文献类型：
--
作者：
Gaudet, Pascale;Argoud-Puy, Ghislaine;Lane, Lydie
与20400个人类蛋白质编码基因相似的大约5000个（25%）目前在蛋白质水平上缺乏任何实验证据。对于许多其他人来说，关于它们的丰度、分布、亚细胞定位、相互作用或细胞功能的信息很少。 HUPO 人类蛋白质组计划（HPP，www.thehpp.org）的目的是收集每种人类蛋白质的信息。 HPP 基于三大支柱：质谱 (MS)、抗体/亲和捕获试剂 (Ab) 和生物信息学驱动的知识库 (KB)。为了实现这一目标，以染色体为中心的人类蛋白质组计划 (C-HPP) 提议通过主要关注目前缺乏 MS 证据或 Ab 检测的蛋白质来逐个染色体地构建此目录 (www.c-hpp.org)。这些被 HPP 联盟称为“缺失的蛋白质”。缺乏对蛋白质的观察可能是由于多种因素造成的，包括不正确和不完整的基因注释、低表达或受限表达或不稳定。 neXtProt (www.nextprot.org) 是一个专门针对人类蛋白质的新的基于网络的知识平台，旨在通过精心挑选的基因组变异、翻译后修饰以及组织和细胞中蛋白质表达的高通量实验获得的详细信息来补充 UniProtKB/Swiss-Prot (www.uniprot.org)。本文介绍了 neXtProt 如何帮助优先考虑 C-HPP 工作并将 C-HPP 结果与其他研究工作相结合以创建完整的人类蛋白质组目录。
About 5000 (25%) of the similar to 20400 human protein-coding genes currently lack any experimental evidence at the protein level. For many others, there is only little information relative to their abundance, distribution, subcellular localization, interactions, or cellular functions. The aim of the HUPO Human Proteome Project (HPP, www.thehpp.org) is to collect this information for every human protein. HPP is based on three major pillars: mass spectrometry (MS), antibody/affinity capture reagents (Ab), and bioinformatics-driven knowledge base (KB). To meet this objective, the Chromosome-Centric Human Proteome Project (C-HPP) proposes to build this catalog chromosome-by-chromosome (www.c-hpp.org) by focusing primarily on proteins that currently lack MS evidence or Ab detection. These are termed "missing proteins" by the HPP consortium. The lack of observation of a protein can be due to various factors including incorrect and incomplete gene annotation, low or restricted expression, or instability. neXtProt (www.nextprot.org) is a new web-based knowledge platform specific for human proteins that aims to complement UniProtKB/Swiss-Prot (www.uniprot.org) with detailed information obtained from carefully selected high-throughput experiments on genomic variation, post-translational modifications, as well as protein expression in tissues and cells. This article describes how neXtProt contributes to prioritize C-HPP efforts and integrates C-HPP results with other research efforts to create a complete human proteome catalog.