Interfacing cellular networks of S. cerevisiae and E. coli: Connecting dynamic and genetic information

BMC Genomics

Research Article

Frank Emmert-Streib¹  Ricardo de Matos Simoes¹  Matthias Dehmer² 

[1] Computational Biology and Machine Learning Laboratory Center for Cancer Research and Cell Biology School of Medicine, Dentistry and Biomedical Sciences Faculty of Medicine, Health and Life Sciences Queen’s University Belfast, 97 Lisburn Road, Belfast, UK;Institute for Bioinformatics and Translational Research UMIT, Hall in Tyrol, Tyrol, Austria;

关键词: Gene Ontology;    Cellular Network;    Gene Regulatory Network;    Transcriptional Regulatory Network;    Gene Ontology Term;   

DOI  :  10.1186/1471-2164-14-324

 received in 2012-07-31, accepted in 2013-04-25,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundIn 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.ResultsWe 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.ConclusionsAlthough 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.

【 授权许可】

Unknown   
© de Matos Simoes et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.