Simulated gene expression time series for 55 genes and 30 timepoints generated as in Lebre et al (2010). In the simulation model, every gene may be target gene but only genes 51 to 55 are parent genes.
This dataset was produced by Lucau-Danila et al. (2005). In this study the authors measured the changes in the mRNA concentrations for each gene at successive times after addition of an antimitotic drug (benomyl), in the growth media of Saccharomyces cerevisiae cells. Parallel experiments were conducted in different genetic contexts: the wild type strain and knock out (KO) strains in which the genes coding for different transcription factors connected to drug response (YAP1, PDR1, PDR3 and YRR1) were deleted. For 78 genes, the measured expression values for 5 different time points (at 30s, 2min, 4min, 10min and 20min) are available, in each yeast strains (WT, DeltaYAP1, DeltaPDR1, DeltaPDR3 and DeltaYRR1). These genes are divided into 18 clusters of genes with condordant transcription profiles. In this context, regulatory associations between parent and target genes are proposed if the deletion of a parent gene significantly alters the expression measurements of the target genes.
Set of possible priors used in the ARTIVAsubnet function for the number of changepoints (resp. incoming edges) according to a given number of maximum changepoints maxCP (resp. incoming Edges maxPred) when parameters (alphaCP, betaCP for the CPs or alphaEdges, betaEdges for the edges) in function ARTIVAsubnet are set to default (alpha=1, beta=0.5). In the ARTIVAsubnet procedure, the number of CPs (respectively the number of incoming edges) is sampled from a truncated Poisson with mean lambda, where lambda is drawn from an Inverse Gamma distribution (alpha, beta), see Lebre et al. (2010) for more details.
Gene expression time series for 4028 genes involved in the life cycle of Drosophila melanogaster. The microarray data measured gene expression levels during all four major stages of morphogenesis: embryo, larva, pupa and adult (67 time points). Data published in Arbeitman et al. (2002) and used in Lebre et al. (2010)
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