TIGRESS swMATH ID: 23826 Software Authors: Haury, A.C., Mordelet, F., Vera-Licona, P., Vert, J.P. Description: TIGRESS: Trustful Inference of Gene REgulation using Stability Selection. BACKGROUND: Inferring the structure of gene regulatory networks (GRN) from a collection of gene expression data has many potential applications, from the elucidation of complex biological processes to the identification of potential drug targets. It is however a notoriously difficult problem, for which the many existing methods reach limited accuracy. RESULTS: In this paper, we formulate GRN inference as a sparse regression problem and investigate the performance of a popular feature selection method, least angle regression (LARS) combined with stability selection, for that purpose. We introduce a novel, robust and accurate scoring technique for stability selection, which improves the performance of feature selection with LARS. The resulting method, which we call TIGRESS (for Trustful Inference of Gene REgulation with Stability Selection), was ranked among the top GRN inference methods in the DREAM5 gene network inference challenge. In particular, TIGRESS was evaluated to be the best linear regression-based method in the challenge. We investigate in depth the influence of the various parameters of the method, and show that a fine parameter tuning can lead to significant improvements and state-of-the-art performance for GRN inference, in both directed and undirected settings. CONCLUSIONS: TIGRESS reaches state-of-the-art performance on benchmark data, including both in silico and in vivo (E. coli and S. cerevisiae) networks. This study confirms the potential of feature selection techniques for GRN inference. Code and data are available on http://cbio.ensmp.fr/tigress. Moreover, TIGRESS can be run online through the GenePattern platform (GP-DREAM, http://dream.broadinstitute.org). Homepage: https://www.ncbi.nlm.nih.gov/pubmed/23173819 Related Software: SIRENE; ARACNE; glasso; JASPAR; BioGRID; glmnet; mmpp; GeneNetWeaver; Path2Models; SOSlib; LASSIE; BioPreDyn-bench; MMG; sgnesR; GeNGe; SGN Sim; IntaRNA; CopraRNA; IntScore; SINCERITIES Cited in: 9 Publications all top 5 Cited by 31 Authors 1 Akaho, Shotaro 1 Beinrucker, Andre 1 Bischl, Bernd 1 Blanchard, Gilles 1 d’Alché-Buc, Florence 1 Doğan, Ürün 1 Engström, Christopher 1 Grebogi, Celso 1 Hepp, Tobias 1 Hinkelmann, Franziska 1 Hino, Hideitsu 1 Hu, Gang 1 Huynh-Thu, Vân Anh 1 Iwasaki, Taishi 1 Johansson, Patrik 1 Lai, Yingcheng 1 Laubenbacher, Reinhard C. 1 Mayr, Andreas 1 Michailidis, George C. 1 Murata, Noboru 1 Murrugarra, David 1 Nelander, Sven 1 Sanguinetti, Guido 1 Silvestrov, Sergei D. 1 Swartling, Fredrik J. 1 Tatsuno, Masami 1 Thomas, Janek 1 Veliz-Cuba, Alan 1 Wang, Wenxu 1 Weishaupt, Holger 1 Zhang, Chaoyang all top 5 Cited in 7 Serials 1 Mathematical Biosciences 1 Physics Letters. A 1 Physics Reports 1 Neural Networks 1 Computational & Mathematical Methods in Medicine 1 Statistics and Computing 1 Methods in Molecular Biology all top 5 Cited in 8 Fields 6 Biology and other natural sciences (92-XX) 2 Combinatorics (05-XX) 2 Statistics (62-XX) 2 Information and communication theory, circuits (94-XX) 1 Dynamical systems and ergodic theory (37-XX) 1 Probability theory and stochastic processes (60-XX) 1 Mechanics of particles and systems (70-XX) 1 Game theory, economics, finance, and other social and behavioral sciences (91-XX) Citations by Year