A skellam model to identify differential patterns of gene expression induced by environmental signals

BMC Genomics
Libo JiangRongling Wu

Abstract

RNA-seq, based on deep-sequencing techniques, has been widely employed to precisely measure levels of transcripts and their isoforms expressed under different conditions. However, robust statistical tools used to analyze these complex datasets are lacking. By grouping genes with similar expression profiles across treatments, cluster analysis provides insight into gene functions and networks that have become increasingly important. We proposed and verified a cluster algorithm based on a skellam model for grouping genes into distinct groups based on the pattern of gene expression in response to changing conditions or in different tissues. This algorithm capitalizes on the skellam distribution to capture the count property of RNA-seq data and clusters genes in different environments. A two-stage hierarchical expectation-maximization (EM) algorithm was implemented to estimate the optimal number of groups and mean expression levels of each group across two environments. A procedure was formulated to test whether and how a given group shows a plastic response to environmental changes. The model was used to analyze an RNA-seq dataset measured from reciprocal crosses of early Arabidopsis thaliana embryos that respond differently based ...Continue Reading

References

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Citations

Feb 20, 2016·Scientific Reports·Ningtao WangRongling Wu
Aug 2, 2015·BMC Genomics·Rong LuGrzegorz A Rempala
Oct 3, 2020·Computational and Structural Biotechnology Journal·Libo JiangRongling Wu

Related Concepts

Impacts, Environmental
Two-Parameter Models
Arabidopsis thaliana <plant>
MRNA Differential Display
Gene Expression Profiles
Gene-Environment Interaction
Statistical Cluster
Embryo
Environment
Gene Clusters

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