Integrative multi-omics module network inference with Lemon-Tree

Eric Bonnet, Laurence Calzone, Tom Michoel

Research output: Contribution to journalArticlepeer-review

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.
Original languageEnglish
Article numbere1003983
JournalPLoS Computational Biology
Volume11
Issue number2
DOIs
Publication statusPublished - 13 Feb 2015

Keywords / Materials (for Non-textual outputs)

  • q-bio.GN

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  • ISP1: Analysis and prediction in complex animal systems

    Tenesa, A. (Principal Investigator), Archibald, A. (Co-investigator), Beard, P. (Co-investigator), Bishop, S. (Co-investigator), Bronsvoort, M. (Co-investigator), Burt, D. (Co-investigator), Freeman, T. (Co-investigator), Haley, C. (Co-investigator), Hocking, P. (Co-investigator), Houston, R. (Co-investigator), Hume, D. (Co-investigator), Joshi, A. (Co-investigator), Law, A. (Co-investigator), Michoel, T. (Co-investigator), Summers, K. (Co-investigator), Vernimmen, D. (Co-investigator), Watson, M. (Co-investigator), Wiener, P. (Co-investigator), Wilson, A. (Co-investigator), Woolliams, J. (Co-investigator), Ait-Ali, T. (Researcher), Barnett, M. (Researcher), Carlisle, A. (Researcher), Finlayson, H. (Researcher), Haga, I. (Researcher), Karavolos, M. (Researcher), Matika, O. (Researcher), Paterson, T. (Researcher), Paton, B. (Researcher), Pong-Wong, R. (Researcher), Robert, C. (Researcher) & Robertson, G. (Researcher)

    BBSRC

    1/04/1231/03/17

    Project: Research

  • Lemon-Tree: Multi-omics module network inference

    Michoel, T. (Developer) & Bonnet, E. (Developer), 2012

    Research output: Non-textual formSoftware

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