Pipeline to uncover additional regulatory layers. Step 1: Identify conditions linked to the main regulatory event for the initial gene set. This can be done using biclustering techniques or by direct comparison with the expression levels of the regulator (if known). Step 2: Build co-expression networks in the remaining conditions. Step 3: Identify the closest neighbours of the selected genes in the new networks. Step 4: iterative round of motif identification/matching to identify the secondary motif and the set of genes with this motif in their upstream regions.