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However, our current knowledge about the gene regulatory mechanisms that are governed by extracellular signals is severely limited.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>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.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1752-0509-6-38","type":"journal-article","created":{"date-parts":[[2012,5,14]],"date-time":"2012-05-14T16:17:40Z","timestamp":1337012260000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma"],"prefix":"10.1186","volume":"6","author":[{"given":"Ricardo","family":"de Matos Simoes","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shailesh","family":"Tripathi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frank","family":"Emmert-Streib","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,5,14]]},"reference":[{"key":"899_CR1","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1038\/ng873","volume":"31","author":"N Guelzim","year":"2002","unstructured":"Guelzim N, Bottani S, Bourgine P, Kepes F: Topological and causal structure of the yeast transcriptional regulatory network. 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