Discovering temporal patterns of differential gene expression in microarray time series
Oliver Stegle, K Denby, S McHattie, S Meade, David L. Wild, Zoubin Ghahramani and Karsten Borgwardt
In: German Conference on Bioinformatics 2009, 28-30 SEP 2009, Halle, Germany.
A wealth of time series of microarray measurements have become available
over recent years. Several two-sample tests for detecting differential gene expression
in these time series have been defined, but they can only answer the question whether a
gene is differentially expressed across the whole time series, not in which intervals it is
differentially expressed. In this article, we propose a Gaussian process based approach
for studying these dynamics of differential gene expression. In experiments on Arabidopsis
thaliana gene expression levels, our novel technique helps us to uncover that
the family of WRKY transcription factors appears to be involved in the early response
to infection by a fungal pathogen.