Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W263-70. doi: 10.1093/nar/gks541. Epub 2012 Jun 11.
A module is a fundamental unit forming with highly connected proteins and performs a certain kind of biological functions. Modules and module-module interaction (MMI) network are essential for understanding cellular processes and functions. The MoNetFamily web server can identify the modules, homologous modules (called module family) and MMI networks across multiple species for the query protein(s). This server first finds module candidates of the query by using BLASTP to search the module template database (1785 experimental and 1252 structural templates). MoNetFamily then infers the homologous modules of the selected module candidate using protein-protein interaction (PPI) families. According to homologous modules and PPIs, we statistically calculated MMIs and MMI networks across multiple species. For each module candidate, MoNetFamily identifies its neighboring modules and their MMIs in module networks of Homo sapiens, Mus musculus and Danio rerio. Finally, MoNetFamily shows the conserved proteins, PPI profiles and functional annotations of the module family. Our results indicate that the server can be useful for MMI network (e.g. 1818 modules and 9678 MMIs in H. sapiens) visualizations and query annotations using module families and neighboring modules. We believe that the server is able to provide valuable insights to determine homologous modules and MMI networks across multiple species for studying module evolution and cellular processes. The MoNetFamily sever is available at http://monetfamily.life.nctu.edu.tw.
模块是由高度连接的蛋白质形成的基本单位，执行特定的生物学功能。模块和模块-模块相互作用（MMI）网络对于理解细胞过程和功能至关重要。MoNetFamily 服务器可以跨多个物种识别查询蛋白质的模块、同源模块（称为模块家族）和 MMI 网络。该服务器首先使用 BLASTP 搜索模块模板数据库（1785 个实验和 1252 个结构模板），为查询找到模块候选者。MoNetFamily 然后使用蛋白质-蛋白质相互作用（PPI）家族推断选定模块候选者的同源模块。根据同源模块和 PPIs，我们在跨多个物种的统计计算了 MMIs 和 MMI 网络。对于每个模块候选者，MoNetFamily 识别其在 Homo sapiens、Mus musculus 和 Danio rerio 模块网络中的相邻模块及其 MMIs。最后，MoNetFamily 显示了模块家族的保守蛋白质、PPI 图谱和功能注释。我们的结果表明，该服务器可用于 MMI 网络（例如，Homo sapiens 中的 1818 个模块和 9678 个 MMIs）可视化和使用模块家族和相邻模块查询注释。我们相信，该服务器能够提供有价值的见解，用于确定跨多个物种的同源模块和 MMI 网络，以研究模块进化和细胞过程。MoNetFamily 服务器可在 http://monetfamily.life.nctu.edu.tw 访问。
