title: Integrative multi-omics module network inference with Lemon-Tree.
abstract: Module network inference is an established statistical method to reconstruct co-expression modules and their upstream regulatory programs from integrated multi-omics datasets measuring the activity levels of various cellular components across different individuals, experimental conditions or time points of a dynamic process. We have developed Lemon-Tree, an open-source, platform-independent, modular, extensible software package implementing state-of-the-art ensemble methods for module network inference. We benchmarked Lemon-Tree using large-scale tumor datasets and showed that Lemon-Tree algorithms compare favorably with state-of-the-art module network inference software. We also analyzed a large dataset of somatic copy-number alterations and gene expression levels measured in glioblastoma samples from The Cancer Genome Atlas and found that Lemon-Tree correctly identifies known glioblastoma oncogenes and tumor suppressors as master regulators in the inferred module network. Novel candidate driver genes predicted by Lemon-Tree were validated using tumor pathway and survival analyses. Lemon-Tree is available from http://lemon-tree.googlecode.com under the GNU General Public License version 2.0.
authors: Institut Curie, Paris, France; INSERM U900, Paris, France; Mines ParisTech, Fontainebleau, France.
authors: Eric
authors: E
authors: Bonnet
authors: Institut Curie, Paris, France; INSERM U900, Paris, France; Mines ParisTech, Fontainebleau, France.
authors: Laurence
authors: L
authors: Calzone
authors: Division of Genetics & Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, United Kingdom.
authors: Tom
authors: T
authors: Michoel
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005909:Glioblastoma / Q000235:genetics / Q000378:metabolism / Q000401:mortality; D006801:Humans; D020407:Internet; D053208:Kaplan-Meier Estimate; D015398:Signal Transduction / Q000235:genetics; D012984:Software