Fig. 1

ChIP-Seq analysis identifies genomic binding sites of TBX2 in E14.5 lungs. a, b Analysis of TBX2 ChIP-sequencing peaks with Genomic Regions Enrichment of Annotations Tool (GREAT, version 4.0.4). a Bar diagram showing the orientation and distance of TBX2 ChIP peaks to a transcription start site (TSS). b Functional annotation shows enrichment of genes associated with TBX2 ChIP peaks in clusters with annotated mouse phenotypes and biological processes sorted by − log10 binomial p-value. c De-novo motif analysis was performed in Galaxy using FIMO—Scan a set of sequences for motifs (Galaxy v4.11.1.0) Novel consensus sequences are highlighted in colored boxes and compared to known motifs with TomTom Motif Comparison Tool v5.1.1. One palindromic and one non-palindromic motif with similarities to a known TBX2 binding element in the Jaspar database were discovered with E-values of 5.9e−198 and 4.6e−152 (grey boxes). Additional novel palindromic sequences show similarities to a TBX21 binding site in the footprint database, E = 1.7e−252 (green box), an ETS (Jaspar database) and homeobox (footprint database) binding motif, E = 6.8e−497 (red box), and an HMG-Box binding site (footprintDB), E = 4.4e−300 (blue box). e Analysis of motif localization by GREAT discovered conjunct motifs for TBX2 (green), ETS/homeobox (red) and HMG-box proteins (blue) in TBX2 ChIP-Seq peaks. Motifs are colored as in c and colored boxes in d reflect spatial arrangement and interconnection of motifs on both DNA strands (+ and −)