Journal Article

A multivariate Poisson-log normal mixture model for clustering transcriptome sequencing data

Subedi, Sanjeena, Rothstein, Steven J., Silva, Anjali, McNicholas, Paul D.

2019

Overview

Background High-dimensional data of discrete and skewed nature is commonly encountered in high-throughput sequencing studies. Analyzing the network itself or the interplay between genes in this type of data continues to present many challenges. As data visualization techniques become cumbersome for higher dimensions and unconvincing when there is no clear separation between homogeneous subgroups within the data, cluster analysis provides an intuitive alternative. The aim of applying mixture model-based clustering in this context is to discover groups of co-expressed genes, which can shed light on biological functions and pathways of gene products. Results A mixture of multivariate Poisson-log normal (MPLN) model is developed for clustering of high-throughput transcriptome sequencing data. Parameter estimation is carried out using a Markov chain Monte Carlo expectation-maximization (MCMC-EM) algorithm, and information criteria are used for model selection. Conclusions The mixture of MPLN model is able to fit a wide range of correlation and overdispersion situations, and is suited for modeling multivariate count data from RNA sequencing studies. All scripts used for implementing the method can be found at https://github.com/anjalisilva/MPLNClust .

• Publisher: BioMed Central,BioMed Central Ltd,BMC
• Subject: Algorithms / Bioinformatics / Biomedical and Life Sciences / Clustering / Co-expression networks / Computational biology / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Discrete data / Genes / Genetic research / Information visualization / Life Sciences / Markov chain Monte Carlo / Markov processes / Methodology / Methodology Article / Methods / Microarrays / Monte Carlo methods / Multivariate analysis / Multivariate Poisson-log normal distribution / Nature / Poisson processes / RNA / RNA sequencing / Transcriptome analysis / Visualization (Computer)