Figure 2

Combining different sources of information to visually assess putative transcription factor binding sites. (A) The sequence view shows matches to the position weight matrix of the Su(Hw) insulator protein (blue bars) in a portion of the 3 Mb Adh region of D. melanogaster. The validity of these matches is supported by a chromatin immunoprecipitation (ChIP) experiment with microarray detection. The track underneath the sequence view shows ChIP enrichment for Su(Hw) along a 1 kb tiling path. (B) On the nucleotide level, Su(Hw) sites show a good degree of conservation although they are generally located in lowly conserved regions. Sequence conservation is here displayed using phastCon scores. The Su(Hw) position weight matrix matches were generated with Patser and loaded through the BioSAVE plug-in system; the phastCon scores were supplied as GFF file.