Inference algorithms for gene networks: a statistical mechanics analysis

TitleInference algorithms for gene networks: a statistical mechanics analysis
Publication TypeJournal Article
Year of Publication2008
AuthorsBraunstein A, Pagnani A, Weigt M, Zecchina R
JournalJournal of Statistical Mechanics: Theory and Experiment
PaginationP12001 (29pp)

The inference of gene regulatory networks from high throughput gene expression data is one of the major challenges in systems biology. This paper aims at analysing and comparing two different algorithmic approaches. The first approach uses pairwise correlations between regulated and regulating genes; the second one uses message-passing techniques for inferring activating and inhibiting regulatory interactions. The performance of these two algorithms can be analysed theoretically on well-defined test sets, using tools from the statistical physics ofdisordered systems like the replica method. We find that the second algorithm outperforms the first one since it takes into account collective effects of multiple regulators.