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

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Interfacing cellular networks of S. cerevisiae and E. coli : Connecting dynamic and genetic information. / Matos Simoes, Ricardo de; Dehmer, Matthias; Emmert-Streib, Frank.

In: BMC Genomics, Vol. 14, No. 1, 324, 11.05.2013.

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Matos Simoes, Ricardo de ; Dehmer, Matthias ; Emmert-Streib, Frank. / Interfacing cellular networks of S. cerevisiae and E. coli : Connecting dynamic and genetic information. In: BMC Genomics. 2013 ; Vol. 14, No. 1.

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@article{8ac1266904ea4391876cc663a36c2f30,
title = "Interfacing cellular networks of S. cerevisiae and E. coli: Connecting dynamic and genetic information",
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.",
author = "{Matos Simoes}, {Ricardo de} and Matthias Dehmer and Frank Emmert-Streib",
year = "2013",
month = "5",
day = "11",
doi = "10.1186/1471-2164-14-324",
language = "English",
volume = "14",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "Springer Verlag",
number = "1",

}

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TY - JOUR

T1 - Interfacing cellular networks of S. cerevisiae and E. coli

T2 - Connecting dynamic and genetic information

AU - Matos Simoes, Ricardo de

AU - Dehmer, Matthias

AU - Emmert-Streib, Frank

PY - 2013/5/11

Y1 - 2013/5/11

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84877302557&partnerID=8YFLogxK

U2 - 10.1186/1471-2164-14-324

DO - 10.1186/1471-2164-14-324

M3 - Article

VL - 14

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 324

ER -