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• W2029387041 abstract "Abstract Background 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. Results 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. Conclusions 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 physical periphery of the cell. In addition, we identify a variety of novel pathological transmembrane proteins such as ion channel complexes and signaling receptors in B-cell lymphoma." @default.
• W2029387041 created "2016-06-24" @default.
• W2029387041 creator A5005661878 @default.
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• W2029387041 date "2012-05-14" @default.
• W2029387041 modified "2023-10-18" @default.
• W2029387041 title "Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma" @default.
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• W2029387041 doi "https://doi.org/10.1186/1752-0509-6-38" @default.
• W2029387041 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3476434" @default.
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