title: Inferring contagion in regulatory networks.
abstract: Several gene regulatory network models containing concepts of directionality at the edges have been proposed. However, only a few reports have an interpretable definition of directionality. Here, differently from the standard causality concept defined by Pearl, we introduce the concept of contagion in order to infer directionality at the edges, i.e., asymmetries in gene expression dependences of regulatory networks. Moreover, we present a bootstrap algorithm in order to test the contagion concept. This technique was applied in simulated data and, also, in an actual large sample of biological data. Literature review has confirmed some genes identified by contagion as actually belonging to the TP53 pathway.
authors.affiliation: A. Fujita is with the Computational Science Research Program, RIKEN, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. andrefujita@riken.jp
authors.forename: André
authors.initials: A
authors.lastname: Fujita
authors.forename: João Ricardo
authors.initials: JR
authors.lastname: Sato
authors.forename: Marcos
authors.initials: M
authors.lastname: Angelo
authors.forename: Almeida
authors.initials: A
authors.lastname: Demasi
authors.forename: Rui
authors.initials: R
authors.lastname: Yamaguchi
authors.forename: Teppei
authors.initials: T
authors.lastname: Shimamura
authors.forename: Carlos Eduardo
authors.initials: CE
authors.lastname: Ferreira
authors.forename: Mari Cleide
authors.initials: MC
authors.lastname: Sogayar
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyano
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016159:Tumor Suppressor Protein p53 / Q000235:genetics
chemical_list: D016159:Tumor Suppressor Protein p53