Systematic differences in signal emitting and receiving revealed by PageRank analysis of a human protein interactome.
Systematic differences in signal emitting and receiving revealed by PageRank analysis of a human protein interactome.
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人类蛋白质相互作用组的Pagerank分析揭示了信号发出和接收的系统差异。
DOI：
10.1371/journal.pone.0044872
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Li XQ
中科院分区：
文献类型：
--
作者：
Du D;Lee CF;Li XQ
大多数蛋白质 PageRank 研究不使用蛋白质相互作用中的信号流方向信息，因为直到最近才能在大型蛋白质数据库中轻松获得此信息。因此，有四个问题有待回答：A）蛋白质相互作用组中信号发射和接收之间的一般区别是什么？ B) 哪些蛋白质在定向排名中名列前茅？ C) 高等级蛋白质比低等级蛋白质在进化上更保守吗？ D) 具有相似排序的蛋白质是否往往具有相似的亚细胞位置？在本研究中，我们使用前向、反向和非定向 PageRank 方法来解决这些问题，对人类蛋白质的信息定向网络进行排名并研究其进化保守性。正向排名对信息接收者给予信用，反向排名对信息发送者给予信用，无向排名主要根据交互次数进行排名。正向和非定向排序生成的蛋白质列表高度相关，但反向和非定向排序生成的蛋白质列表则不然。结果表明，人类蛋白质相互作用组中信号发射/接收系统的特点是关键发射和相对均匀的接收。信号通路蛋白常见于排名靠前的蛋白中。八种蛋白质既是信息的顶部发射器又是顶部接收器。除了少数与物种相关的新功能蛋白质外，排名靠前的蛋白质在进化上都非常保守。蛋白质亚基排名位置反映了亚基功能。这些结果证明了不同 PageRank 方法在表征蛋白质网络方面的有用性，并为细胞中蛋白质相互作用提供了见解。
Most protein PageRank studies do not use signal flow direction information in protein interactions because this information was not readily available in large protein databases until recently. Therefore, four questions have yet to be answered: A) What is the general difference between signal emitting and receiving in a protein interactome? B) Which proteins are among the top ranked in directional ranking? C) Are high ranked proteins more evolutionarily conserved than low ranked ones? D) Do proteins with similar ranking tend to have similar subcellular locations? In this study, we address these questions using the forward, reverse, and non-directional PageRank approaches to rank an information-directional network of human proteins and study their evolutionary conservation. The forward ranking gives credit to information receivers, reverse ranking to information emitters, and non-directional ranking mainly to the number of interactions. The protein lists generated by the forward and non-directional rankings are highly correlated, but those by the reverse and non-directional rankings are not. The results suggest that the signal emitting/receiving system is characterized by key-emittings and relatively even receivings in the human protein interactome. Signaling pathway proteins are frequent in top ranked ones. Eight proteins are both informational top emitters and top receivers. Top ranked proteins, except a few species-related novel-function ones, are evolutionarily well conserved. Protein-subunit ranking position reflects subunit function. These results demonstrate the usefulness of different PageRank approaches in characterizing protein networks and provide insights to protein interaction in the cell.
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影响因子：
3.4
作者：
Polden, Julie;McManus, Ciara A.;Dunn, Michael J.
通讯作者：
Dunn, Michael J.
影响因子：
5.8
作者：
Kuang, R;Weston, J;Leslie, C
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Leslie, C
影响因子：
46.9
作者：
Schwikowski, B;Uetz, P;Fields, S
通讯作者：
Fields, S
影响因子：
3
作者：
Krallinger M;Vazquez M;Leitner F;Salgado D;Chatr-Aryamontri A;Winter A;Perfetto L;Briganti L;Licata L;Iannuccelli M;Castagnoli L;Cesareni G;Tyers M;Schneider G;Rinaldi F;Leaman R;Gonzalez G;Matos S;Kim S;Wilbur WJ;Rocha L;Shatkay H;Tendulkar AV;Agarwal S;Liu F;Wang X;Rak R;Noto K;Elkan C;Lu Z;Dogan RI;Fontaine JF;Andrade-Navarro MA;Valencia A
通讯作者：
Valencia A
影响因子：
11.5
作者：
Sebolt-Leopold, Judith S.
通讯作者：
Sebolt-Leopold, Judith S.