During the last couple of years, we have mapped gene regulatory networks in Arabidopsis using a variety of experimental and computational methods. Apart from developing a transcription factor (TF)-target gene identification workflow based on the integration of novel protein-binding microarray data and multi-species promoter sequence conservation, we have also mapped regulatory interactions using >30 ChIP-Seq data sets. We actively develop new comparative methods to identify conserved non-coding sequences in dicots and monocots and have demonstrated how these show high specificity to map functional TF-target genes in plants. Whereas initial network analysis focused on the model species Arabidopsis, we are in the process of expanding our network portfolio to other dicots (e.g. poplar, soybean) and are exploring new opportunities to perform network-based gene analysis in cereals as well (maize, wheat).