Skip to Main content Skip to Navigation
Journal articles

SegCorr a statistical procedure for the detection of genomic regions of correlated expression

Abstract : Background: Detecting local correlations in expression between neighboring genes along the genome has proved to be an effective strategy to identify possible causes of transcriptional deregulation in cancer. It has been successfully used to illustrate the role of mechanisms such as copy number variation (CNV) or epigenetic alterations as factors that may significantly alter expression in large chromosomal regions (gene silencing or gene activation). Results: The identification of correlated regions requires segmenting the gene expression correlation matrix into regions of homogeneously correlated genes and assessing whether the observed local correlation is significantly higher than the background chromosomal correlation. A unified statistical framework is proposed to achieve these two tasks, where optimal segmentation is efficiently performed using dynamic programming algorithm, and detection of highly correlated regions is then achieved using an exact test procedure. We also propose a simple and efficient procedure to correct the expression signal for mechanisms already known to impact expression correlation. The performance and robustness of the proposed procedure, called SegCorr, are evaluated on simulated data. The procedure is illustrated on cancer data, where the signal is corrected for correlations caused by copy number variation. It permitted the detection of regions with high correlations linked to epigenetic marks like DNA methylation. Conclusions: SegCorr is a novel method that performs correlation matrix segmentation and applies a test procedure in order to detect highly correlated regions in gene expression.
Complete list of metadata

Cited literature [44 references]  Display  Hide  Download
Contributor : Myriam Bodescot Connect in order to contact the contributor
Submitted on : Wednesday, March 6, 2019 - 4:37:54 PM
Last modification on : Friday, August 5, 2022 - 2:38:10 PM
Long-term archiving on: : Friday, June 7, 2019 - 6:05:56 PM


Publisher files allowed on an open archive


Distributed under a Creative Commons Attribution - ShareAlike 4.0 International License



Eleni Ioanna Delatola, Emilie Lebarbier, Tristan Mary-Huard, François Radvanyi, Stéphane Robin, et al.. SegCorr a statistical procedure for the detection of genomic regions of correlated expression. BMC Bioinformatics, BioMed Central, 2017, 18 (1), pp.333. ⟨10.1186/s12859-017-1742-5⟩. ⟨inserm-02059501⟩



Record views


Files downloads