Projects per year
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 language | English |
---|---|
Article number | e1003983 |
Journal | PLoS Computational Biology |
Volume | 11 |
Issue number | 2 |
DOIs | |
Publication status | Published - 13 Feb 2015 |
Keywords
- q-bio.GN
Fingerprint
Dive into the research topics of 'Integrative multi-omics module network inference with Lemon-Tree'. Together they form a unique fingerprint.Projects
- 1 Finished
-
ISP1: Analysis and prediction in complex animal systems
Tenesa, A., Archibald, A., Beard, P., Bishop, S., Bronsvoort, M., Burt, D., Freeman, T., Haley, C., Hocking, P., Houston, R., Hume, D., Joshi, A., Law, A., Michoel, T., Summers, K., Vernimmen, D., Watson, M., Wiener, P., Wilson, A., Woolliams, J., Ait-Ali, T., Barnett, M., Carlisle, A., Finlayson, H., Haga, I., Karavolos, M., Matika, O., Paterson, T., Paton, B., Pong-Wong, R., Robert, C. & Robertson, G.
1/04/12 → 31/03/17
Project: Research
Research output
- 1 Software
-
Lemon-Tree: Multi-omics module network inference
Michoel, T. & Bonnet, E., 2012Research output: Non-textual form › Software
Activities
- 1 Participation in conference
-
EMBO Symposium: From Single to Multi-Omics
Tom Michoel (Participant)
12 Nov 2017 → 14 Nov 2017Activity: Participating in or organising an event types › Participation in conference