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

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Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma. / de Matos Simoes, Ricardo; Tripathi, Shailesh; Emmert-Streib, Frank.

In: BMC Systems Biology, Vol. 6, 38, 14.05.2012.

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de Matos Simoes, Ricardo ; Tripathi, Shailesh ; Emmert-Streib, Frank. / Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma. In: BMC Systems Biology. 2012 ; Vol. 6.

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@article{4a0d6dfa273244008c007bc139fd1d9d,
title = "Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma.",
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 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.",
keywords = "B-cell lymphoma, Gene expression data, Gene regulatory network, Statistical network inference",
author = "{de Matos Simoes}, Ricardo and Shailesh Tripathi and Frank Emmert-Streib",
year = "2012",
month = "5",
day = "14",
doi = "10.1186/1752-0509-6-38",
language = "English",
volume = "6",
journal = "BMC Systems Biology",
issn = "1752-0509",
publisher = "Springer Verlag",

}

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TY - JOUR

T1 - Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma.

AU - de Matos Simoes, Ricardo

AU - Tripathi, Shailesh

AU - Emmert-Streib, Frank

PY - 2012/5/14

Y1 - 2012/5/14

N2 - 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 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.

AB - 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 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.

KW - B-cell lymphoma

KW - Gene expression data

KW - Gene regulatory network

KW - Statistical network inference

UR - http://www.scopus.com/inward/record.url?scp=84865119369&partnerID=8YFLogxK

U2 - 10.1186/1752-0509-6-38

DO - 10.1186/1752-0509-6-38

M3 - Article

VL - 6

JO - BMC Systems Biology

JF - BMC Systems Biology

SN - 1752-0509

M1 - 38

ER -