Motif Enrichment Analyses Obtained By Centrimo On Human Enhancers

We applied Centrimo (Bailey and Machanick 2012) from the MEME suite version 4.11.1 with default parameters to DNA sequences of regions ± 500 bp around the mid-points of enhancers from class 1 (lower %GC) and class 2 (higher %GC). Class 1 enhancer regions were used as foreground and class 2 enhancer regions as background and vice-versa. The MEME databases of motifs<br> considered for enrichment were derived from (Jolma et al. 2013) (jolma2013.meme), JASPAR (Mathelier et al. 2015a) (JASPAR_CORE_2016_vertebrates.meme), Cis-BP (Weirauch et al. 2014) (Homo_sapiens.meme), Swiss Regulon (Pachkov et al. 2013) (Swiss_Regulon_human_and_mouse.meme), and HOCOMOCO (Kulakovskiy et al. 2016) (HOCOMOCOv10_HUMAN_mono_meme_format.meme). The same procedure was applied to promoter regions ( ± 500 bp around gene starts) associated with class 1 and class 2 enhancers.