Figure 1.

Mixed miRNA/TF Feed-Forward Loops and CircuitsDB construction pipeline. a) Representation of a typical mixed Feed-Forward regulatory Loop (FFL) included in CircuitsDB. Circuits are composed by a master Transcription Factor (TF, square box) that regulates a microRNA (miRNA, diamond-shaped box) and together with it a Joint Target protein-coding gene (round box). Inside each circuit, -• indicates transcriptional activation/repression, whilst ⊣ post-transcriptional repression. b) Flow-chart of the strategy used for the construction of CircuitsDB. We first built a genome-wide catalogue of putative core promoter regions for protein-coding and miRNA genes, plus a set of 3'-UTRs for protein-coding genes, in human and mouse. Then we used the analysis pipeline developed in our previous work [13] to infer a dataset of mixed regulatory FFLs, in human and mouse. Finally we integrated different kinds of biological annotations to support the circuits' properties; the CircuitsDB web-site allows a dynamic exploration of such properties.