QPath: a method for querying pathways in a protein-protein interaction network.
QPath: a method for querying pathways in a protein-protein interaction network.
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QPATH：一种在蛋白质 - 蛋白质相互作用网络中查询途径的方法。
DOI：
10.1186/1471-2105-7-199
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发表时间：
2006-04-10
影响因子：
3
通讯作者：
Sharan, R
中科院分区：
文献类型：
--
作者：
Shlomi, T;Segal, D;Ruppin, E;Sharan, R
序列比较是生物学研究中最突出的工具之一，并且有助于研究基因功能和进化。用于测量蛋白质相互作用的高通量技术的快速开发要求将这种基本操作扩展到蛋白质网络中的途径水平。
我们提出了使用途径查询的蛋白质网络搜索的综合框架。如果是线性查询途径和感兴趣的网络，我们的算法，QPATH，有效地搜索了网络以获取同源途径，从而允许在已确定的途径中插入和删除蛋白质。匹配的途径根据其使用的蛋白质插入和缺失，其组成蛋白与查询蛋白的序列相似性以及其组成相互作用的可靠性，根据查询途径的变化自动评分。我们使用酵母菌的271种推定途径的广泛收集来将QPATH系统地推断出蛋白质途径。 Q Path确定了69个保守途径，其成员在功能上富集并相干表达。所得的途径倾向于保留原始查询途径的功能，从而使我们能够在苍蝇中获得保守蛋白途径的第一个注释图。
使用QPATH的途径同源性搜索提供了一种强大的方法来识别具有生物学意义的途径并推断其功能。公共数据库中蛋白质相互作用的量增长强调了我们网络查询框架对采矿蛋白质网络数据的重要性。
Sequence comparison is one of the most prominent tools in biological research, and is instrumental in studying gene function and evolution. The rapid development of high-throughput technologies for measuring protein interactions calls for extending this fundamental operation to the level of pathways in protein networks. We present a comprehensive framework for protein network searches using pathway queries. Given a linear query pathway and a network of interest, our algorithm, QPath, efficiently searches the network for homologous pathways, allowing both insertions and deletions of proteins in the identified pathways. Matched pathways are automatically scored according to their variation from the query pathway in terms of the protein insertions and deletions they employ, the sequence similarity of their constituent proteins to the query proteins, and the reliability of their constituent interactions. We applied QPath to systematically infer protein pathways in fly using an extensive collection of 271 putative pathways from yeast. QPath identified 69 conserved pathways whose members were both functionally enriched and coherently expressed. The resulting pathways tended to preserve the function of the original query pathways, allowing us to derive a first annotated map of conserved protein pathways in fly. Pathway homology searches using QPath provide a powerful approach for identifying biologically significant pathways and inferring their function. The growing amounts of protein interactions in public databases underscore the importance of our network querying framework for mining protein network data.
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影响因子：
12.3
作者：
Breitkreutz BJ;Stark C;Tyers M
通讯作者：
Tyers M
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：
14.9
作者：
Drysdale RA;Crosby MA;FlyBase Consortium
通讯作者：
FlyBase Consortium
DOI：
10.1145/210332.210337
发表时间：
1995-07-01
期刊：
JOURNAL OF THE ASSOCIATION FOR COMPUTING MACHINERY
影响因子：
--
作者：
ALON, N;YUSTER, R;ZWICK, U
通讯作者：
ZWICK, U
影响因子：
7
作者：
Matthews, LR;Vaglio, P;Vidal, M
通讯作者：
Vidal, M