PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles.
PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles.
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DOI：
10.1093/nar/gkv452
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发表时间：
2015-07-01
影响因子：
14.9
通讯作者：
Tabach Y
中科院分区：
文献类型：
--
作者：
Sadreyev IR;Ji F;Cohen E;Ruvkun G;Tabach Y
在相同途径、蛋白质复合物或相同环境条件下发挥作用的蛋白质可以在系统发育分支中表现出相似的序列保守模式。在不再需要特定蛋白质复合物或途径的物种中，这些蛋白质作为一个整体往往会丢失或分化。对大量真核生物序列保守模式的相似性进行分析可以预测不同蛋白质之间的功能关联，识别新的途径成员并揭示以前未表征的蛋白质的功能。我们使用标准化的系统发育分析来预测蛋白质功能并识别新的途径成员和疾病基因。人类、小鼠、秀丽隐杆线虫和果蝇基因组中数万个保守蛋白的系统发育谱可以在我们的新网络服务器 PhyloGene 上查询。 PhyloGene 提供直观且用户友好的平台来查询 86 种动物、真菌、植物和原生生物基因组的保护模式。可以通过从深入研究的物种的全基因组蛋白质集中选择名称或输入蛋白质序列来提交蛋白质查询。图形输出显示了查询的序列保守性概况以及所选基因组中蛋白质的最相似的系统发育概况。用户还可以以数字形式下载此输出。
Proteins that function in the same pathways, protein complexes or the same environmental conditions can show similar patterns of sequence conservation across phylogenetic clades. In species that no longer require a specific protein complex or pathway, these proteins, as a group, tend to be lost or diverge. Analysis of the similarity in patterns of sequence conservation across a large set of eukaryotes can predict functional associations between different proteins, identify new pathway members and reveal the function of previously uncharacterized proteins. We used normalized phylogenetic profiling to predict protein function and identify new pathway members and disease genes. The phylogenetic profiles of tens of thousands conserved proteins in the human, mouse, Caenorhabditis elegans and Drosophila genomes can be queried on our new web server, PhyloGene. PhyloGene provides intuitive and user-friendly platform to query the patterns of conservation across 86 animal, fungal, plant and protist genomes. A protein query can be submitted either by selecting the name from whole-genome protein sets of the intensively studied species or by entering a protein sequence. The graphic output shows the profile of sequence conservation for the query and the most similar phylogenetic profiles for the proteins in the genome of choice. The user can also download this output in numerical form.
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影响因子：
64.5
作者：
Schwartz S;Agarwala SD;Mumbach MR;Jovanovic M;Mertins P;Shishkin A;Tabach Y;Mikkelsen TS;Satija R;Ruvkun G;Carr SA;Lander ES;Fink GR;Regev A
通讯作者：
Regev A
影响因子：
9.9
作者：
Tabach, Yuval;Golan, Tamar;Ruvkun, Gary
通讯作者：
Ruvkun, Gary
影响因子：
64.8
作者：
Tabach, Yuval;Billi, Allison C.;Ruvkun, Gary
通讯作者：
Ruvkun, Gary
ORM家族蛋白介导鞘脂稳态。
影响因子：
64.8
作者：
Breslow, David K.;Collins, Sean R.;Bodenmiller, Bernd;Aebersold, Ruedi;Simons, Kai;Shevchenko, Andrej;Ejsing, Christer S.;Weissman, Jonathan S.
通讯作者：
Weissman, Jonathan S.
影响因子：
64.5
作者：
Pagliarini DJ;Calvo SE;Chang B;Sheth SA;Vafai SB;Ong SE;Walford GA;Sugiana C;Boneh A;Chen WK;Hill DE;Vidal M;Evans JG;Thorburn DR;Carr SA;Mootha VK
通讯作者：
Mootha VK