Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma.
Research output: Contribution to journal › Article › Scientific › peer-review
Details
| Original language | English |
|---|---|
| Article number | 38 |
| Journal | BMC Systems Biology |
| Volume | 6 |
| DOIs | |
| Publication status | Published - 14 May 2012 |
| Publication type | A1 Journal article-refereed |
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.
ASJC Scopus subject areas
Keywords
- B-cell lymphoma, Gene expression data, Gene regulatory network, Statistical network inference