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.
data(dream4)networkBMA