NGS Analysis: From raw reads to biological interpretation.

ChIP-Seq – Finding regulatory motifs and extracting downstream targets


The first steps in the ChIP-Seq workflow are mapping the reads and subsequently applying peak detection. Genomatix offers various methods for peak calling (supporting the use of control files) with all of them returning a list of statistically significant peaks.


For many transcription factors (TFs) DNA-binding motifs have been published in the scientific literature. Genomatix has been collecting such motifs for many years in MatBase, our transcription factor knowledge base. These motifs can be found in peaks and promotors using MatInspector, which enables us to automatically extract overrepresented TF binding sites in detected peaks. In addition we identify pairs of TFs that bind with a specific distance profile and may have synergistic functions in gene regulation.


To uncover novel TF binding sites CoreSearch is applied. Overall, the workflow allows to generate TF binding site motifs directly from your data with only a few mouse clicks.


To understand the functional relevance of detected peaks, you can extract possible target genes by correlating peaks with promoter regions or primary transcripts. This enables you to uncover biological processes and canonical pathways regulated through the targeted factor by using the Genomatix Pathway System (GePS).