Contains six objects: dream4gold10, dream4gold100, dream4ts10, dream4ts100, dream4wild10, dream4wild100, each in the form of a list of matrices, in which each element corresponds to one of 5 different datasets. dream4gold10 and dream4gold100 are lists of gold standard network specifications for the 10-gene and 100-gene simulated networks. The list elements are three-column data frames, in which the first and second column represent all possible regulator-gene pairs in the network, excluding self edges. The third column is a boolean variable indicating whether or not the genes in the first two columns are a regulatory pair and thus consitute an edge in the network. dream4ts10 and dream4ts100 are lists of time course datasets showing how the simulated network responds to a perturbation and how it relaxes upon removal of the perturbation. For both size 10 and size 100, 5 different datasets are available. For networks of size 10, each of the 5 datasets consists of 5 different time series replicates, and for networks of size 100, each of the 5 datasets consists of 10 time series replicates. Each time series has 21 time points. In both cases, there are 5 list components corresponding to the datasets, each of which is a data frame in which the first two columns give the replicate and time, and the remaining columns give the measured expression levels. The initial condition always corresponds to a steady-state measurement of the wild-type. At t=0, a perturbation is applied to the network as described below. The first half of the time series (until t=500) shows the response of the network to the perturbation. At t=500, the perturbation is removed (the wild-type network is restored). The second half of the time series (until t=1000) shows how the gene expression levels go back from the perturbed to the wild-type state. dream4wild10 and dream4wild100 are lists giving the steady state (wild-type) expression levels for the genes in each dataset.
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