Table 2.

Summary of TFs that profit from considering DNA methylation in the motif models. For each TF, we list the availability of ChIP-seq data sets for the four cell types studied. Columns ‘Methylation’ and ‘Methyl. & Deps.’ indicate a significant and consistent improvement (y: yes, n: no) by including information about methylation in general and/or in combination with modelling intra-motif dependencies, respectively. We also note if a binding motif contains a prominent CpG in its core (CpG) and if methylation sensitivity in the core is larger than outside the core (Core). In the last column, we note references to the literature for TFs that have already been reported to be methylation sensitive, where ‘–’, ‘+’ and ‘s’ indicate negative or positive influence of methylation or general methylation sensitivity according to the referenced publications, respectively

TF	GM12878	HepG2	K562	liver	Methylation	Methyl. & Deps.	CpG	Core	Literature
ARID3A	x	x	x		y	n	n	y	new
ARNT	x	x	x		y	n	y	y	- (30)
ATF3		x	x	x	y	y	y	y	- (23)
ATF7	x	x	x		y	n	y	y	- (23)
BHLHE40	x	x	x		y	n	y	y	- (23)
CREM	x	x	x		y	n	y	y	- (23)
ELF1	x	x	x		y	n	y	y	- (23,60)
FOXA1		x	x	x	y	n	n	n	- (85)
FOXA2		x		x	y	y	n	n	new
FOXK2	x	x	x		y	n	n	y	new
GABPA	x	x	x	x	y	n	y	y	- (23)
HNF4A		x		x	y	y	n	y	new
HNF4G		x		x	y	y	n	y	new
JUND	x	x	x	x	y	y	n	y	- (23)
MAX	x	x	x	x	y	y	y	y	s/- (23,30)
MNT		x	x		y	n	y	y	s/- (30)
NFATC3	x		x		y	n	n	y	+ (23)
NONO		x	x		y	y	y	y	- (86)
NR2C2	x		x		y	n	y	y	new
NRF1	x	x	x		y	n	y	y	- (30)
PKNOX1	x		x		y	n	n	y	new
RAD51	x	x	x		y	y	y	y	new
SIX5	x		x		y	n	y	y	new
SP1		x	x	x	y	y	y	y	+/– (23,70,71–71)
TBL1XR1	x	x	x		y	n	n	y	new
USF2	x		x		y	y	y	y	- (23)
YY1	x	x	x	x	y	n	y	y	different motif (68)
ZBTB40	x		x		y	n	y	y	new