Spatio-temporal model for multiple ChIP-seq experiments
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Saverio Ranciati
,
Cinzia Viroli
Abstract
The increasing availability of ChIP-seq data demands for advanced statistical tools to analyze the results of such experiments. The inherent features of high-throughput sequencing output call for a modelling framework that can account for the spatial dependency between neighboring regions of the genome and the temporal dimension that arises from observing the protein binding process at progressing time points; also, multiple biological/technical replicates of the experiment are usually produced and methods to jointly account for them are needed. Furthermore, the antibodies used in the experiment lead to potentially different immunoprecipitation efficiencies, which can affect the capability of distinguishing between the true signal in the data and the background noise. The statistical procedure proposed consist of a discrete mixture model with an underlying latent Markov random field: the novelty of the model is to allow both spatial and temporal dependency to play a role in determining the latent state of genomic regions involved in the protein binding process, while combining all the information of the replicates available instead of treating them separately. It is also possible to take into account the different antibodies used, in order to obtain better insights of the process and exploit all the biological information available.
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Supplemental Material
The online version of this article (DOI: 10.1515/sagmb-2014-0074) offers supplementary material, available to authorized users.
©2015 by De Gruyter
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Articles in the same Issue
- Frontmatter
- Research Articles
- Study of triplet periodicity differences inside and between genomes
- H-CLAP: hierarchical clustering within a linear array with an application in genetics
- Inferring bi-directional interactions between circadian clock genes and metabolism with model ensembles
- Bayesian inference for Markov jump processes with informative observations
- Likelihood free inference for Markov processes: a comparison
- Spatio-temporal model for multiple ChIP-seq experiments
- Software and Application Note
- GenePEN: analysis of network activity alterations in complex diseases via the pairwise elastic net
- Corrigendum
- Corrigendum to: Simple estimators of false discovery rates given as few as one or two p-values without strong parametric assumptions
