Figure 3

Pipeline to analyze ChIP-seq data. After the locations of the ChIP-seq binding sites have been retrieved, their genomic context is analysed. A core set is defined by selecting targets with i) literature evidence or ii) a hit in the upstream region of not divergently transcribed genes. The expression levels of these genes are analysed and they are categorized through (bi)clustering. Finally the rest of the putative targets are assigned to these groups (if possible) based on the similarities of their expression patterns.