Inferring contagion in regulatory networks

IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):570-76. doi: 10.1109/TCBB.2010.40.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Gene Expression Profiling
  • Gene Regulatory Networks*
  • Genomics / methods*
  • Oligonucleotide Array Sequence Analysis / methods
  • Tumor Suppressor Protein p53 / genetics

Substances

  • Tumor Suppressor Protein p53