This folder contains HOMER (Heinz, 2010) motif analysis results for 4 TFs described in Lizio_et_al.
Known motifs provided with HOMER (v4.6, 3-29-2014) were expanded by importing all known NEUROD1, LMX1A, PAX6 and RFX motifs from Swissregulon, Jaspar, Uniprobe, and Hocomoco, into HOMER before carrying out the scan.
Motif analysis was then carried out following default settings and with the masking of repeat sequences. Target sequences (ChIP-seq peaks) were compared against the whole genome.