Genomic transcription regulatory element location analysis via poisson weighted lasso

Abstract : The distances between DNA Transcription Regulatory Elements (TRE) provide important clues to their dependencies and function within the gene regulation process. However, the locations of those TREs as well as their cross distances between occurrences are stochastic, in part due to the inherent limitations of Next Generation Sequencing methods used to localize them, in part due to biology itself. This paper describes a novel approach to analyzing these locations and their cross distances even at long range via a Poisson random convolution. The resulting deconvolution problem is ill-posed, and sparsity regularization is used to offset this challenge. Unlike previous work on sparse Poisson inverse problems, this paper adopts a weighted LASSO estimator with data-dependent weights calculated using concentration inequalities that account for the Poisson noise. This method exhibits better squared error performance than the classical (unweighted) LASSO both in theoretical performance bounds and in simulation studies, and can easily be computed using off-the-shelf LASSO solvers.
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Communication dans un congrès
Statistical Signal Processing Workshop (SSP), 2016 IEEE, Jun 2016, Palma de Mallorca, Spain. IEEE pp.16263580 2016, 〈10.1109/SSP.2016.7551831〉
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https://hal-agroparistech.archives-ouvertes.fr/hal-01585531
Contributeur : Eva Legras <>
Soumis le : lundi 11 septembre 2017 - 16:01:08
Dernière modification le : vendredi 20 juillet 2018 - 11:13:04

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Xin Jiang, Patricia Reynaud-Bouret, Vincent Rivoirard, Laure Sansonnet, Rebecca Willett. Genomic transcription regulatory element location analysis via poisson weighted lasso. Statistical Signal Processing Workshop (SSP), 2016 IEEE, Jun 2016, Palma de Mallorca, Spain. IEEE pp.16263580 2016, 〈10.1109/SSP.2016.7551831〉. 〈hal-01585531〉

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