Interfacing cellular networks of S. cerevisiae and E. coli: Connecting dynamic and genetic information
Interfacing cellular networks of S. cerevisiae and E. coli: Connecting dynamic and genetic information
复制标题
DOI：
10.1186/1471-2164-14-324
复制
发表时间：
2013-05-11
期刊：
影响因子：
4.4
通讯作者：
Emmert-Streib, Frank
中科院分区：
文献类型：
--
作者：
Simoes, Ricardo de Matos;Dehmer, Matthias;Emmert-Streib, Frank
背景：近年来，各种类型的细胞网络已深入生物学领域，如今在研究真核生物和原核生物时无处不在。然而，现象学基因网络和推断性基因网络之间的关系以及生物学重叠，例如从大规模转录组数据推断出的蛋白质相互作用网络和基因调控网络之间的关系，在很大程度上尚未被探索。
结果：在本研究中，我们对酿酒酵母和大肠杆菌的蛋白质 - 蛋白质网络、转录调控网络和推断的基因调控网络之间的结构、功能和染色体关系进行了深入分析。此外，我们通过比较（例如，利用基因之间可用的相互作用结构来比较基因本体术语的功能共现）研究了这些网络的全局和局部方面以及它们的生物学信息重叠。
结论：尽管各个网络代表了细胞相互作用的不同层面，在全局结构和功能上存在差异，但我们观察到它们的网络接口在蛋白质复合物组装、蛋白质水解、转录、翻译、代谢和调控相互作用方面的关键功能。总体而言，我们的研究结果阐明了这些网络的可整合性以及它们相互关联的生物学过程。
Background: In recent years, various types of cellular networks have penetrated biology and are nowadays used omnipresently for studying eukaryote and prokaryote organisms. Still, the relation and the biological overlap among phenomenological and inferential gene networks, e.g., between the protein interaction network and the gene regulatory network inferred from large-scale transcriptomic data, is largely unexplored.Results: We provide in this study an in-depth analysis of the structural, functional and chromosomal relationship between a protein-protein network, a transcriptional regulatory network and an inferred gene regulatory network, for S. cerevisiae and E. coli. Further, we study global and local aspects of these networks and their biological information overlap by comparing, e.g., the functional co-occurrence of Gene Ontology terms by exploiting the available interaction structure among the genes.Conclusions: Although the individual networks represent different levels of cellular interactions with global structural and functional dissimilarities, we observe crucial functions of their network interfaces for the assembly of protein complexes, proteolysis, transcription, translation, metabolic and regulatory interactions. Overall, our results shed light on the integrability of these networks and their interfacing biological processes.