Integrative multi-omics module network inference with Lemon-Tree.
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 po...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2015-02-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1003983 |
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| _version_ | 1850125577792520192 |
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| author | Eric Bonnet Laurence Calzone Tom Michoel |
| author_facet | Eric Bonnet Laurence Calzone Tom Michoel |
| author_sort | Eric Bonnet |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-d20232e2f2ff4bbda3d549a32fabbbbf |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2015-02-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-d20232e2f2ff4bbda3d549a32fabbbbf2025-08-20T02:34:06ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582015-02-01112e100398310.1371/journal.pcbi.1003983Integrative multi-omics module network inference with Lemon-Tree.Eric BonnetLaurence CalzoneTom MichoelModule 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.https://doi.org/10.1371/journal.pcbi.1003983 |
| spellingShingle | Eric Bonnet Laurence Calzone Tom Michoel Integrative multi-omics module network inference with Lemon-Tree. PLoS Computational Biology |
| title | Integrative multi-omics module network inference with Lemon-Tree. |
| title_full | Integrative multi-omics module network inference with Lemon-Tree. |
| title_fullStr | Integrative multi-omics module network inference with Lemon-Tree. |
| title_full_unstemmed | Integrative multi-omics module network inference with Lemon-Tree. |
| title_short | Integrative multi-omics module network inference with Lemon-Tree. |
| title_sort | integrative multi omics module network inference with lemon tree |
| url | https://doi.org/10.1371/journal.pcbi.1003983 |
| work_keys_str_mv | AT ericbonnet integrativemultiomicsmodulenetworkinferencewithlemontree AT laurencecalzone integrativemultiomicsmodulenetworkinferencewithlemontree AT tommichoel integrativemultiomicsmodulenetworkinferencewithlemontree |