Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma.

BMC Systems Biology
Ricardo de Matos SimoesF Emmert-Streib

Abstract

The physical periphery of a biological cell is mainly described by signaling pathways which are triggered by transmembrane proteins and receptors that are sentinels to control the whole gene regulatory network of a cell. However, our current knowledge about the gene regulatory mechanisms that are governed by extracellular signals is severely limited. The purpose of this paper is three fold. First, we infer a gene regulatory network from a large-scale B-cell lymphoma expression data set using the C3NET algorithm. Second, we provide a functional and structural analysis of the largest connected component of this network, revealing that this network component corresponds to the peripheral region of a cell. Third, we analyze the hierarchical organization of network components of the whole inferred B-cell gene regulatory network by introducing a new approach which exploits the variability within the data as well as the inferential characteristics of C3NET. As a result, we find a functional bisection of the network corresponding to different cellular components. Overall, our study allows to highlight the peripheral gene regulatory network of B-cells and shows that it is centered around hub transmembrane proteins located at the physica...Continue Reading

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Citations

May 15, 2013·BMC Genomics·Ricardo de Matos SimoesFrank Emmert-Streib
Nov 14, 2012·Drug Discovery Today·Paola Lecca, Corrado Priami
May 15, 2015·BMC Systems Biology·Ricardo de Matos SimoesFrank Emmert-Streib
Apr 25, 2019·Current Genomics·Daniel MooreFrank Emmert-Streib
Aug 12, 2017·Journal of Alzheimer's Disease : JAD·Shweta Bagewadi KawaliaMartin Hofmann-Apitius

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Datasets Mentioned

BETA
GSE2350
GSE11318
GSE22470

Methods Mentioned

BETA
chip

Software Mentioned

R
GeNGe
C3NET
topGO
netsim
ARACNE
SynTReN
Bioconductor

Related Concepts

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