Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation


Motivation: Gene expression profiling using RNA-seq is a powerful technique for screening RNA species' landscapes and their dynamics in an unbiased way. While several advanced methods exist for differential expression analysis of RNA-seq data, proper tools to analyze RNA-seq time-course have not been proposed.
Results:In this study, we use RNA-seq to measure gene expression during the early human T helper 17 (Th17) cell differentiation and T-cell activation (Th0). To quantify Th17-specific gene expression dynamics, we present a novel statistical methodology, DyNB, for analyzing time-course RNA-seq data. We use non-parametric Gaussian processes to model temporal correlation in gene expression and combine that with negative binomial likelihood for the count data. To account for experiment-specific biases in gene expression dynamics, such as differences in cell differentiation efficiencies, we propose a method to rescale the dynamics between replicated measurements. We develop an MCMC sampling method to make inference of differential expression dynamics between conditions. DyNB identifies several known and novel genes involved in Th17 differentiation. Analysis of differentiation efficiencies revealed consistent patterns in gene expression dynamics between different cultures. We use qRT-PCR to validate differential expression and differentiation efficiencies for selected genes. Comparison of the results with those obtained via traditional timepoint-wise analysis shows that time-course analysis together with time rescaling between cultures identifies differentially expressed genes which would not otherwise be detected.


The method presented and implemented in this study is available as a MATLAB routine

New: The MCMC sampling for DyNB (without the time scaling, Bayes factor computation, and dispersion estimation) is also available as a Stan routine. (The results reported in the article are obtained with the Matlab implementation.)


Tarmo Äijö
Aalto University School of Science,
Department of Information and Computer Science,
P.O. Box 15400, FI-00076 Aalto, Finland

Updated: May 1, 2015
Updated: August 11, 2014