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

Ricardo D.M. Simoes, Shailesh Tripathi, Frank Emmert-Streib

Research output: Contribution to journalArticlepeer-review

16 Citations (Scopus)

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.

Original languageEnglish
Article number38
Pages (from-to)38
JournalBMC Systems Biology
Volume6
DOIs
Publication statusPublished - 14 May 2012
Externally publishedYes

Keywords

  • B-cell lymphoma
  • Gene expression data
  • Gene regulatory network
  • Statistical network inference
  • Reproducibility of Results
  • Humans
  • Signal Transduction/genetics
  • Gene Expression Regulation, Neoplastic
  • Computational Biology/methods
  • Gene Regulatory Networks
  • Algorithms
  • Cluster Analysis
  • Lymphoma, B-Cell/genetics

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