Supplemental Figure 1.
Fraction
(y
-
axis) of each
cCRE
class (x
-
axis)
with at least one DAP associated
(“bound”) ad those with none in our
dataset (“unbound”) when restricted
to those overlapping with an ATAC
-
seq peak in HepG2.
Supplemental Figure 2.
Dinucleotide
-
matched control regions show reduced
incidence of TF binding. Control regions for
each open chromatin region of a given
cCRE
were generated using the
nullseq_generate.py
function of the LS
-
GKM suite. Overlap of TF binding was then
determined, as for Figure 1A. Bars show
the number of sites of each control group
(x
-
axis) with at least one DAP association
(“bound”) and those with none in out
dataset (“unbound”). Asterisks show
significance of a chi
-
squared test
comparing observed versus control
sequences for bound and unbound sets.
*** p<=2.2E
-
16
** p<=1E
-
8
* p<=0.05
***
***
***
***
***
***
**
ns
Supplemental
Figure
3
.
Barplot
showing
the
number
of
regions
of
each
cCRE
class
bound
(y
-
axis)
as
a
function
of
binned
number
of
DAPs
bound
to
a
region
(x
-
axis)
.
cCRE
classes
are
denoted
by
color
.
PLS
(red),
pELS
(orange),
dELS
(yellow),
CA
-
H
3
K
4
me
3
(pink),
CA
-
CTCF
(blue),
CA
-
TF
(light
green),
TF
(dark
green),
CA
(grey)
.
HOT
sites
are
bound
by
>=
170
of
our
DAPs,
and
thus
represent
a
portion
of
the
101
-
200
bin,
as
well
as
all
higher
bins
.
Supplemental
Figure
4
.
Barplot
showing
the
fraction
of
regions
of
each
cCRE
class
bound
(y
-
axis)
as
a
function
of
binned
number
of
DAPs
bound
to
a
region
(x
-
axis)
.
cCRE
classes
are
denoted
by
color
.
PLS
(red),
pELS
(orange),
dELS
(yellow),
CA
-
H
3
K
4
me
3
(pink),
CA
-
CTCF
(blue),
CA
-
TF
(light
green),
TF
(dark
green),
CA
(grey)
.
HOT
sites
are
bound
by
>=
170
of
our
DAPs,
and
thus
represent
a
portion
of
the
101
-
200
bin,
as
well
as
all
higher
bins
.
Supplemental
Figure
5
.
Boxplot
shows
lentiMPRA
signal
as
denoted
in
Agarwal
et
al
2023
(y
-
axis)
as
a
function
of
binned
number
of
DAPs
bound
(x
-
axis)
in
the
genomic
region
for
promoter
(red)
and
distal
(yellow)
regions,
with
control
sequences
(grey)
for
comparison
.
Boxes
represent
25
-
75
%
quartiles
with
line
indicating
median,
whiskers
extend
to
+/
-
1
.
5
*IQR
(inter
-
quartile
range)
past
the
boxes,
and
points
are
observations
falling
outside
of
this
range
.
Asterisks
denote
p
-
values
comparing
distal
to
promoters
in
each
category
.
*** p<=2.2E
-
16
** p<=1E
-
8
* p<=0.05
When comparing to negative control, all
sets are significant at p<=2.2E
-
16 except for
the promoter group at DAPs 0 (p<=1E
-
8)
and Distal at DAPs 401+ (ns)
***
ns
**
***
***
***
***
***
***
***
***
***