In this study, we leveraged the developmental time series of gene expression in primate brain to investigate the expression of genes associated with neurodevelopmental disorders including ASD, ID and SCZ.
Bayesian Estimation of Temporal Regulation (BETR; [ 89]) was used to analyze the developmental time series, as standard ANOVA is not appropriate due to auto-correlation between time points.
Replicate developmental time series of PP, DL and DF were prepared in the same manner, but sequenced using the Illumina HiSeq platform.
As an illustrative example we use a 10-stage developmental time series from the egg to stage 35 (just before hatching).
We evaluated the technical performance of this framework, and we used it to analyze growth and shape of several canonical Caenorhabditis elegans mutants in a developmental time series.
The developmental time series investigated included pups from embryonic days 13, 15 and 17 and postnatal days 0, 5, and 10.
Clustering of gene expression profiles across the developmental time series was performed in GeneSpring using the K-means algorithm.
We extended our analysis to evaluate the effects of development on paralog usage by characterizing differential expression in a developmental time series of G. raimondii seed (10 40 DPA).
Here we make use of isoform expression profiles over a developmental time series in D.melanogaster [ 22] to identify alternative protein isoforms that have expression profiles indicative of function.
A developmental time series of rice transcriptome data [ 68] (Accession: GSE13988, GSE14298, GSE14299 and GSE14300) was also downloaded from GEO [ 67].
Microarray technology has been widely used in many organisms to understand genome-wide changes in gene expression in response to treatments [ 1], in different organs [ 2], cell-types [ 3] and along developmental time series [ 4].
