Open Access Research article

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

Ricardo de Matos Simoes1, Matthias Dehmer2 and Frank Emmert-Streib1*

Author Affiliations

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

2 Institute for Bioinformatics and Translational Research UMIT, Hall in Tyrol, Tyrol, Austria

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BMC Genomics 2013, 14:324  doi:10.1186/1471-2164-14-324

Published: 11 May 2013

Abstract

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.