Fig. 1

Overview of the CroCo framework. CroCo provides a uniform view on the ENCODE compendia of genome-wide measurements along with global networks derived from structured databases and further resources. a) Data sets in these compendia are classified into a high-dimensional data cube along dimensions such as cell-line species and treatment. b) CroCo uses default or user-defined procedures to define and extract DDRNs resulting in a high-dimensional cube of networks structured along the same dimensions. These networks can be filtered, merged, and combined in various ways to produce new networks. Moreover, networks can be transferred between species via orthology mappings of the network nodes. This enables the prediction of regulatory interactions from one or a set of species to closely related species. Via combination and transfer operations, new networks are defined, thereby enabling the flexible construction of user-specified networks from the compendia