CNAmet is an algorithm and R package to prioritize putative cancer driver genes by integrating copy number, DNA methylation and expression data. Outputs of our algorithm include scores for methylation alteration induced expression, copy number aberration induced expression, a score for their combined effect, and adjacent p-values, which are also multiple hypothesis corrected.
In addition to the CNAmet algorithm, our R package includes the S2N algorithm for the integration of copy number to expression data. The CNAmet algorithm is also implemented as a component in the Anduril bioinformatics framework.
News
Version 1.2.1 of CNAmet for R ≥ 3.0 is available. No other updates in CNAmet so use CNAmet v.1.2 if you don't have R 3.x (24 May 2013)- Small update to user guide. (16 April 2013)
- We have updated results for all four TCGA datasets (links below). (1 March 2013)
- We have added an example cancer data set. (21 January 2013)
- We have added two pages: how-to and frequently asked questions. (22 October 2012)
- Updated glioblastoma analysis results are online. (1 August 2012)
- Version 1.2 of CNAmet is now available. (16 May 2012)
- We have updated the results for all of the available breast, ovarian and colorectal data from the Cancer Genome Atlas. We already have CNAmet results for ovarian online and will shortly have for breast and colorectal cancer. (10 April 2012)
- A hardware failure on July 26th caused our websites to go offline for three days. All services have since been restored. (27 July 2011)
Download
There are three versions of the R package.
- CNAmet_1.2.1_32bit.tar.gz for 32bit Unix (for R ≥ 3.0)
- CNAmet_1.2.1_64bit.tar.gz for 64bit Unix (for R ≥ 3.0)
- CNAmet_1.2_32bit.tar.gz for 32bit Unix
- CNAmet_1.2_64bit.tar.gz for 64bit Unix
- CNAmet_1.1.zip for Windows
Installation and algorithm details are discussed in the user guide and how-to article.
The glioblastoma multiforme (GBM) data, which are used for the case study in the CNAmet article, are also available for download.
- GBM sample data 1 (gene expression, and hypomethylation and copy-number gain calls)
- GBM sample data 2 (gene expression, and hypermethylation and copy-number deletion calls)
Citation
Louhimo, R. and Hautaniemi, S. CNAmet: an R package for integration of copy number, expression and methylation data Bioinformatics (2011) 27(6):887-888.
Miscellany
The source code of the case study written in Anduril script can be found here.
The article contains two case study - one with glioblastoma multiforme (GBM) and the other with ovarian cancer (OV) data. Both belong to larger analyses. The complete GBM data analysis can found as a part of the Anduril framework casestudy which is frequently updated. The ovarian cancer analysis results can be found here.
We invite you to browse and use these results freely, and we request you to cite either the Anduril (for GBM) or CNAmet article (for OV) in such cases.
Related websites
- TCGA glioblastoma analysis including CNAmet results
(updated 26 April 2013) - TCGA ovarian cancer analysis including CNAmet results
(updated 26 April 2013) - TCGA invasive breast carcinoma analysis including CNAmet results
(updated 20 April 2013) - TCGA colorectal carcinoma analysis including CNAmet results
(updated 19 April 2013) - Anduril bioinformatics framework
- API for the Anduril component that uses CNAmet
- Moksiskaan pathway integration tool for Anduril