A core-attachment based method to detect protein complexes in PPI networks.
A core-attachment based method to detect protein complexes in PPI networks.
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DOI：
10.1186/1471-2105-10-169
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发表时间：
2009-06-02
影响因子：
3
通讯作者：
Ng SK
中科院分区：
文献类型：
--
作者：
Wu M;Li X;Kwoh CK;Ng SK
如何检测蛋白质复合物是后基因组时代的一项重要且具有挑战性的任务。随着蛋白质-蛋白质相互作用 (PPI) 数据的增加，我们能够从 PPI 网络中识别蛋白质复合物。然而，目前大多数研究仅基于观察PPI网络中的密集区域可能对应于蛋白质复合物来检测蛋白质复合物，但未能考虑蛋白质复合物内的固有组织。为了深入了解蛋白质复合物的组织，本文提出了一种新颖的基于核心附着的方法（COACH），该方法分两个阶段检测蛋白质复合物。它首先检测蛋白质复合物核心作为蛋白质复合物的“心脏”，然后将附件包含到这些核心中以形成具有生物学意义的结构。我们从两个方面评估和分析我们预测的蛋白质复合物。首先，我们通过将预测的复合体与基准复合体进行比较，对我们提出的方法和现有技术进行全面的比较。其次，我们还使用各种生物学证据和知识来验证核心附着结构。我们提出的 COACH 方法已应用于两种不同的酵母 PPI 网络，实验结果表明 COACH 的性能明显优于最先进的技术。此外，所鉴定的具有核心附着结构的复合物被证明与现有的生物学知识非常匹配，从而为未来的生物学研究提供更多见解。
How to detect protein complexes is an important and challenging task in post genomic era. As the increasing amount of protein-protein interaction (PPI) data are available, we are able to identify protein complexes from PPI networks. However, most of current studies detect protein complexes based solely on the observation that dense regions in PPI networks may correspond to protein complexes, but fail to consider the inherent organization within protein complexes. To provide insights into the organization of protein complexes, this paper presents a novel core-attachment based method (COACH) which detects protein complexes in two stages. It first detects protein-complex cores as the "hearts" of protein complexes and then includes attachments into these cores to form biologically meaningful structures. We evaluate and analyze our predicted protein complexes from two aspects. First, we perform a comprehensive comparison between our proposed method and existing techniques by comparing the predicted complexes against benchmark complexes. Second, we also validate the core-attachment structures using various biological evidence and knowledge. Our proposed COACH method has been applied on two different yeast PPI networks and the experimental results show that COACH performs significantly better than the state-of-the-art techniques. In addition, the identified complexes with core-attachment structures are demonstrated to match very well with existing biological knowledge and thus provide more insights for future biological study.
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影响因子：
56.9
作者：
Kim, Philip M.;Lu, Long J.;Gerstein, Mark B.
通讯作者：
Gerstein, Mark B.
影响因子：
3
作者：
Altaf-Ul-Amin, Md;Shinbo, Yoko;Kanaya, Shigehiko
通讯作者：
Kanaya, Shigehiko
影响因子：
64.8
作者：
Gavin, AC;Bösche, M;Superti-Furga, G
通讯作者：
Superti-Furga, G
影响因子：
64.8
作者：
Gavin, AC;Aloy, P;Superti-Furga, G
通讯作者：
Superti-Furga, G
影响因子：
3.3
作者：
Fraering, P;Imhof, I;Conzelmann, A
通讯作者：
Conzelmann, A