Mixture model with multiple allocations for clustering spatially correlated observations in the analysis of ChIP-Seq data

DOI10.1002/BIMJ.201600131zbMATH Open1379.62082arXiv1601.04879OpenAlexW2309401466WikidataQ38700845 ScholiaQ38700845MaRDI QIDQ4597923FDOQ4597923

Authors: Saverio Ranciati, Cinzia Viroli, Ernst C. Wit 

Publication date: 14 December 2017

Published in: Biometrical Journal (Search for Journal in Brave)

Abstract: Model-based clustering is a technique widely used to group a collection of units into mutually exclusive groups. There are, however, situations in which an observation could in principle belong to more than one cluster. In the context of Next-Generation Sequencing (NGS) experiments, for example, the signal observed in the data might be produced by two (or more) different biological processes operating together and a gene could participate in both (or all) of them. We propose a novel approach to cluster NGS discrete data, coming from a ChIP-Seq experiment, with a mixture model, allowing each unit to belong potentially to more than one group: these multiple allocation clusters can be flexibly defined via a function combining the features of the original groups without introducing new parameters. The formulation naturally gives rise to a `zero-inflation group' in which values close to zero can be allocated, acting as a correction for the abundance of zeros that manifest in this type of data. We take into account the spatial dependency between observations, which is described through a latent Conditional Auto-Regressive process that can reflect different dependency patterns. We assess the performance of our model within a simulation environment and then we apply it to ChIP-seq real data.

Full work available at URL: https://arxiv.org/abs/1601.04879

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zbMATH Keywords

model-based clusteringmixture modelspatial dependencyChIP-Seqmultiple allocations

Mathematics Subject Classification ID

Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10)

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