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

Ricardo de Matos Simoes, Matthias Dehmer, Frank Emmert-Streib

Research output: Contribution to journalArticle

17 Citations (Scopus)
198 Downloads (Pure)

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.
Original languageEnglish
Article number324
Number of pages23
JournalBMC Genomics
Volume14
DOIs
Publication statusPublished - 11 May 2013

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