Fig. 5

High-confidence DV enhancers identify novel DV target genes. a All MEs and DEEs that were confirmed by high occupancy of DV transcription factors and differential target gene expression by mRNA-seq. The occupancy of DV transcription factors Dl, Twi, Sna, Zen, Mad, and Zld is shown as a heatmap of normalized ChIP enrichment over input. The enhancers were categorized based on the function of their target genes (transcription factors, signaling, morphogenesis, other) and whether they have high occupancy of Dl, Mad (green and light brown bars, respectively), which indicates that they are likely direct targets of the signaling cascade. b A selection of MEs and DEEs that were confirmed by in vivo reporter expression of overlapping Vienna Tiles (VTs), which match the expression pattern of the assigned target gene. In situ hybridization images for VTs were obtained from Kvon et al. [39]. Unless noted otherwise, the in situ hybridization images for target genes are from the BDGP database [73–75]. The CadN expression pattern is by Biemar et al. [17], copyright (2006) National Academy of Sciences, USA; that of be is from Fly-FISH [76, 77] and was color-modified to resemble the black-and-white in situ hybridization images, reused with permission; that of Wnt2 is from Russell et al. [78] Copyright 1992 The Company of Biologists, and that of Stat92E is from Yan et al. [79], reprinted from Yan et al., Identification of a Stat gene that functions in Drosophila development. Cell, 84(3):421–430, Copyright 1996, with permission from Elsevier