supplemental figures s1-s10 emanuelsson et al.. figure s1a number of nts in tars (placenta)...
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Supplemental Figures S1-S10Emanuelsson et al.
Figure S1aNumber of nts in TARs (placenta)
Emanuelsson et al.
TAR Generation Threshold (percentile)
Num
ber
of N
ucle
otid
es in
TA
Rs
Figure S1bNumber of nts in TARs (NB4)
Emanuelsson et al.
TAR Generation Threshold (percentile)
Num
ber
of N
ucle
otid
es in
TA
Rs
Figure S2aAssessing the performance of different MAS scoring schemes – placenta
Emanuelsson et al.
sensitivity=tp/(tp+fn)
ppv=
tp/(
tp+
fp)
Figure S2bAssessing the performance of different MASscoring schemes – NB4
Emanuelsson et al.
sensitivity=tp/(tp+fn)
ppv=
tp/(
tp+
fp)
Figure S3PPV vs. sensitivity for MAS-N and Affy NB4 data,varying the segmentation threshold from 70th to 99th
Emanuelsson et al.
sensitivity=tp/(tp+fn)
ppv=
tp/(
tp+
fp)
Figure S4asens/PPV vs Gencode; placenta MAS stranded
Emanuelsson et al.
sensitivity=tp/(tp+fn)
ppv=
tp/(
tp+
fp)
Figure S4bsens/PPV vs Gencode; placenta MAS strands merged
Emanuelsson et al.
sensitivity=tp/(tp+fn)
ppv=
tp/(
tp+
fp)
Figure S5asens/PPV vs Gencode; NB4 MAS stranded
Emanuelsson et al.
sensitivity=tp/(tp+fn)
ppv=
tp/(
tp+
fp)
Figure S5bsens/PPV vs Gencode; NB4 MAS strands merged
Emanuelsson et al.
sensitivity=tp/(tp+fn)
ppv=
tp/(
tp+
fp)
Figure S6aLength distribution (percentage) of TARs
length (nt)
Placenta MAS-N
Placenta MAS-B
Placenta Affy
NB4 MAS-N
NB4 Affy
Emanuelsson et al.
Figure S6bDistribution of number of probes per TAR
number of probes
num
ber
of T
AR
s
<
Placenta MAS-N
Placenta MAS-B
Placenta Affy
NB4 MAS-N
NB4 Affy
Emanuelsson et al.
Figure S7aDistribution of Exon and Intron Median ScoresPlacenta MAS-B (red=intron, blue=exon)
Figure S7bDistribution of Exon and Intron Median ScoresPlacenta MAS-N (red=intron, blue=exon)
Figure S7cDistribution of Exon and Intron Median ScoresPlacenta Affy (red=intron, blue=exon)
Figure S7dDistribution of Exon and Intron Median ScoresNB4 MAS-N (red=intron, blue=exon)
Figure S7eDistribution of Exon and Intron Median ScoresNB4 Affy (red=intron, blue=exon)
265 67 325
240 108128
207
701 629
684
47 38 175
52 7185
38
222 369
245
33 25 135
32 4853
26
143 262
160
18 22 111
19 4248
13
106 223
121
Figure S8a
I III
IVII
[Total] [Exon ovlp]
[Conserved region ovlp] [Exon and conserved region ovlp]
Placenta (MAS and Affy)
Placenta MAS-N
Placenta MAS-B
Placenta Affy
NB4 MAS-N
NB4 Affy
Emanuelsson et al.
Overlap of TAR sets (kbp)
455 177 452632 629
Figure S8b
105 86 178190 263
65 58 145125 205 41 50 110 91 160
I [Total] III [Exon ovlp]
II [Conserved region ovlp] IV [Exon and conserved region ovlp]
NB4 (MAS and Affy)
Emanuelsson et al.Placenta MAS-N
Placenta MAS-B
Placenta Affy
NB4 MAS-N
NB4 Affy
Overlap of TAR sets (kbp)
104 228 51
64 57305
267
632
684
28 57 13
32 15105
94
222 190
245
19 44 9
20 1465
63
143 125
160
14 26 6
17 1050
47
107 91
121
Figure S8c
701
I [Total] III [Exon ovlp]
II [Conserved region ovlp] IV [Exon and conserved region ovlp]
MAS (placenta and NB4)
Emanuelsson et al.Placenta MAS-N
Placenta MAS-B
Placenta Affy
NB4 MAS-N
NB4 Affy
Overlap of TAR sets (kbp)
296 333 296629 629
Figure S8d
157 212 51369 263
103 159 45262 205 85 138 22 223 160
I [Total] III [Exon ovlp]
II [Conserved region ovlp] IV [Exon and conserved region ovlp]
Affy (placenta and NB4)
Emanuelsson et al.Placenta MAS-N
Placenta MAS-B
Placenta Affy
NB4 MAS-N
NB4 Affy
Overlap of TAR sets (kbp)
Figure S9a
num
ber
of e
xons
cov
ered
by
TA
R
fraction of exon length covered
Emanuelsson et al.
Placenta MAS-N
Placenta MAS-B
Placenta Affy
NB4 MAS-N
NB4 Affy
Placenta MAS-N
Placenta MAS-B
Placenta Affy
NB4 MAS-N
NB4 Affy
Figure S9b
fraction of exon length covered
perc
enta
ge o
f 5'
exo
ns c
over
ed b
y T
AR
Emanuelsson et al.
Placenta MAS-N
Placenta MAS-B
Placenta Affy
NB4 MAS-N
NB4 Affy
Figure S9c
perc
enta
ge o
f 3'
exo
ns c
over
ed b
y T
AR
fraction of exon length covered
Emanuelsson et al.
Placenta MAS-N
Placenta MAS-B
Placenta Affy
NB4 MAS-N
NB4 Affy
Figure S10a
fraction of TAR length covered
perc
enta
ge o
f ge
nic
and
inte
rgen
ic T
AR
sco
vere
d by
con
serv
ed e
lem
ents
MAS genic TARs
MAS intergenic TARs
Affymetrix genic TARs
Affymetrix intergenic TARs
0-0.10
0.90-1.00
80
70
60
50
40
30
20
10
0
90
0.30-0.40
0.60-0.70
Placenta
Emanuelsson et al.
Figure S10bpe
rcen
tage
of
geni
c an
d in
terg
enic
TA
Rs
cove
red
by c
onse
rved
ele
men
ts
fraction of TAR length covered
MAS genic TARs
MAS intergenic TARs
Affymetrix genic TARs
Affymetrix intergenic TARs
0-0.10
0.30-0.40
0.90-1.00
80
70
60
50
40
30
20
10
0
90
0.60-0.70
NB4
Emanuelsson et al.