the genomic landscape and pharmacogenomic interactions of
TRANSCRIPT
Cell Systems, Volume 6
Supplemental Information
The Genomic Landscape and Pharmacogenomic
Interactions of Clock Genes
in Cancer Chronotherapy
Youqiong Ye, Yu Xiang, Fatma Muge Ozguc, Yoonjin Kim, Chun-Jie Liu, Peter K.Park, Qingsong Hu, Lixia Diao, Yanyan Lou, Chunru Lin, An-YuanGuo, Bingying Zhou, LiWang, Zheng Chen, Joseph S. Takahashi, Gordon B. Mills, Seung-Hee Yoo, and Leng Han
Gene Expression
T/N pairs
Transcriptional dysregulation (Fig.1)
Tumor samplesDisruption of circadi-an rhythm (Fig. 4)
Time points RNAseq data of MCF7 & MCF10A
genes with circadian oscillationNumber of genes correlated with clock genes (T-N)
|log2(T/N Expression)| > 0.58 & FDR < 0.05
RPPA Pathway score
Groups with low or high expression of clock genes
Effects of clock genes on signaling pathways (Fig. 2)
Clinical Data:patient survival, tumor subtypes and stages
Interaction between clock genes and CAGs (Fig.6)
Protein-protein interaction dataChIP-seq data
MutationDNA methylation
Genetic alteration of clock genes (Fig. 3)
Gene expression in CCLEPharmacogenomic data (CTRP)
Time points RNAseq data of CRY2 KD or WT in MEF cells
Therapeutic liability of clock genes (Fig. 7)
Correlation between drug sensitivity and expression of clock genes
TCG
A da
ta: c
linic
al a
nd m
olec
ular
sig
natu
res
in 3
2 ca
ncer
type
s
Raw data | Data produced intermediate stepsResults
Clinical relevance of clock genes (Fig. 5)
GDSC gene expression &Pharmacogenomic data
Figure S1. Related to STAR Methods.The pipeline of bioinformatics analysis procedures and data used for each part of the analysis. Clinically actionable genes (CAGs), The Cancer Genome Atlas (TCGA), Reverse Phase Protein Array (RPPA), The Cancer Cell Line Encyclopedia (CCLE), Genomic of Drug Sensitivity in Cancer (GDSC), Cancer Therapeutics Response Portal (CTRP), Tumor (T), Normal (N), Knock Down (KD), Wild Type (WT), False discovery rate (FDR). The abbreviation for cancer types is listed in table S1.
ACC
BLCA
BRCA
CESC
CHOL
COAD
DLB
CESCA
GBM
HNSC
KICH
KIRC
KIRP
LGG
LIHC
LUAD
LUSC
MESO
OV
PAAD
PCPG
PRAD
READ
SARC
SKCM
STAD
TGCT
THCA
THYM
UCE
C
UCS
UVM
A
B
Activation Inhibition None
●
●
●
●
●
●
●
●●●●●●
●
●
●
●
●
●
●
●
●
●●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●●
●●
●
●
●
●
●
●●●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●●
●
●●
●
●
●●●
●
●
●●
●
●
●●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●●
●
●●
●
●
●●●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●●
●
●
●
●
●
●
●
●
●
●●
●
●●
●
●
●
●
●
●
●
●
●●
●●
●
●
●
●
●
●●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●●
●
●
●
●
RORCRORBRORA
CRY2
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
● ● ● ●
●
●
●●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
● ●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
● ●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
● ●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
● ● ● ●
●
●
●●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
● ●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
● ●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●●
●
●
●
●
●
●
●
●
● ●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
RORA & RORC RORB & RORCRORA & RORB
RORA & RORB & RORC
BLC
ABR
CA
CES
CC
OAD
ESC
AH
NSC
KIR
CKI
RP
LGG
LIH
CLU
ADLU
SCM
ESO OV
PAAD
PCPG
PRAD
REA
DSA
RC
SKC
MST
ADTG
CT
THC
ATH
YMU
CEC
ApoptosisCell Cycle
DNA Damage ResponseEMT
Hormone aHormone b
PI3K/AKTRAS/MAPK
RTKTSC/mTOR
ApoptosisCell Cycle
DNA Damage ResponseEMT
Hormone aHormone b
PI3K/AKTRAS/MAPK
RTKTSC/mTOR
ApoptosisCell Cycle
DNA Damage ResponseEMT
Hormone aHormone b
PI3K/AKTRAS/MAPK
RTKTSC/mTOR
BLC
ABR
CA
CES
CC
OAD
ESC
AH
NSC
KIR
CKI
RP
LGG
LIH
CLU
ADLU
SCM
ESO OV
PAAD
PCPG
PRAD
REA
DSA
RC
SKC
MST
ADTG
CT
THC
ATH
YMU
CEC
BLC
ABR
CA
CES
CC
OAD
ESC
AH
NSC
KIR
CKI
RP
LGG
LIH
CLU
ADLU
SCM
ESO OV
PAAD
PCPG
PRAD
REA
DSA
RC
SKC
MST
ADTG
CT
THC
ATH
YMU
CEC
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
● ●
CRY1 & CRY2
●
●
●
●
●
●
● ●
●
●
●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
CRY1
ApoptosisCell Cycle
DNA Damage ResponseEMT
Hormone aHormone b
PI3K/AKTRAS/MAPK
RTKTSC/mTOR
−log10(FDR)
● ● ●
0.05
0.01
1e−4
−1.0
−0.5
0.0
0.5
1.0
Difference
0 1000 2000
0.0
0.2
0.4
0.6
0.8
1.0
ESCA − RORA & RORC
Survival in days
HighLow
p = 0.043
0 2000 4000 6000
0.0
0.2
0.4
0.6
0.8
1.0
HNSC − RORA & RORC
Survival in days
HighLow
p = 0.044
0 1000 2000 3000
0.0
0.2
0.4
0.6
0.8
1.0
KIRC − RORA & RORC
Survival in days
HighLow
p = 4e−08
0 1000 2000 3000
0.0
0.2
0.4
0.6
0.8
1.0
LIHC − RORA & RORC
Survival in days
HighLow
p = 0.029
C
Surv
ival
rate
Surv
ival
rate
Surv
ival
rate
Surv
ival
rate
AHR
ALAS
1
BHLH
E40
BHLH
E41
BTR
C
CR
EB1
CR
EBBP
CSE
1L
CSN
K1D
CSN
K1E
CSN
K2A1
CSN
K2A2
CSN
K2B
DBP
EP30
0
FBXL
21
FBXL
3
FBXW
11
GN
B2L1
GSK
3B
HLF
IFN
A1
NFI
L3
NO
NO
NR
1I3
PAR
P1
PPAR
A
PPAR
G
PPP1
CA
PPP1
CC
PPP5
C
PRKA
A2
PRKC
A
SIR
T1
TEF
TNF
WD
R5
Apoptosis
Cell Cycle
DNA Damage Response
EMT
Hormone a
Hormone b
PI3K/AKT
RAS/MAPK
RTK
TSC/mTOR
Figure S2. Related to Figure 2. Clock genes associated with the activity of key signaling pathways. (A) Percentage of cancer types with 37 clock genes associated with the activation (red) or inhibition (blue) of key signaling pathways. (B) The difference of pathway scores in key signaling pathways between tumor samples with low expression and high expression of individual or paralog clock genes of CRY1/2, and RORA/B/C. The colors and size of point represent the difference and statistical significance (FDR) of protein-expression pathway scores. (C) Survival analysis for combination of RORA and RORC in ESCA, HNSC, KIRC and LIHC (blue: low expression in both genes; red: high expression in both genes).
A
Neg
ativ
e
Spe
arm
an C
orre
latio
n C
oeffi
cien
t
B
Posi
tive
BLC
APA
ADU
VMPC
PG LGG
MES
OTH
CA
SKC
MSA
RC
BRC
AKI
RP
PRAD
KIR
CAC
CKI
CH
CES
CST
ADES
CA
REA
DC
OAD
HN
SCLU
SCU
CEC
LUAD
LIH
CU
CS
GBM
THYM
TGC
T
TNFFBXL21BTRCTEFARNTL2HLFCSNK2BPARP1WDR5PER3PRKAA2PPARGBHLHE41SIRT1NR1D2CRY2NPAS2ARNTLNR1D1CSE1LCREB1NONOPPARABHLHE40EP300PPP5CCREBBPPRKCAALAS1RORBAHRGNB2L1CSNK2A1PPP1CARORCNR1I3PER1DBPPPP1CCCSNK2A2PER2GSK3B
Figure S3. Related to Figure 3. Epigenetic alterations in clock genes. (A) Correlation between promot-er DNA methylation levels and gene expression across clock genes. (B) Differential DNA methylation level of clock genes between paired tumor and normal samples. (Different beta-value > 0.2, FDR < 0.05, Red: up-regulation; blue: downregulation; size: p value)
● ● ● ●●
● ● ●●
●● ● ●●
● ●● ●
●● ●● ●●
● ●●
● ●●● ●
● ● ● ●
● ● ●
●●● ●● ●●●
● ● ●
●
PRADSTADKIRC
ESCABLCACOADKIRP
HNSCLIHC
LUADTHCABRCAKICH
LUSC
HLF
RO
RA
PER
1PE
R3
RO
RB
CRY
2TE
FPR
KAA2
PER
2FB
XL3
PPAR
GN
FIL3
NR
1I3
FBXL
21R
OR
CC
RY1
PRKC
ATN
FPP
ARA
ALAS
1N
R1D
2SI
RT1
BHLH
E41
CLO
CK
CR
EB1
CSN
K2B
FBXW
11BH
LHE4
0C
SNK2
A2BT
RC
EP30
0IF
NA1
PPP1
CC
PPP5
CC
REB
BPC
SNK1
DG
NB2
L1AR
NTL
CSN
K2A1
GSK
3BPP
P1C
AW
DR
5N
PAS2
AHR
DBP
NO
NO
PAR
P1C
SNK1
EN
R1D
1C
SE1L
ARN
TL2
−0.4−0.200.20.4
B−Value Change
●
●
●
●
P value0.0510−5
10−10
< 10−15
−3053
−2−17
−2055
−660
−280
−3419
−2650
−449
−1319
−1−7
−311
−340
−1
−2312
−1948
66
−1
−1
1
−1264
−1
−1−695
−1
−2838
−744
−2573
−4663
−113
−1−935
−1760
−3310
−3649
−1
−3562
−2067
−3531
−1
−1
−1873
−2833
−3398
−3050
−3879
−3239
−35
−815
−1
−2158
−30−22
−1397
−1828
−1318
−3727
−1919
−2
−1894
−1−270
−1183
−1274
−4
−2526
−508
−3050
−1301
−10
−1655
−3960
−1705
−2610−1735
−310
−1004
−2834
−682
−2465
−2481
−453−2132
−2045
−1241
−3217
17
−2581
−2746
−144
14
−2859
−2609
−61
−1424
−2254
8
−2125
−82
−2042
26
−1806
−20143
0
−82
−715
−2524
−815
73
135
−671−153
−802
−2027
−69
−1767
−2838
−2240
12
−32
−210
−2229
−1553
−404−11
−3476
−2051
−1674
−1334
−3011
−575
−2405−667
37
−1596
−3656
−1
−1611
−2824
−3840
8
−106
−1402
−3307
−2051
−2502
−3405
−1391
504
−142
796
−887
49−319
−266
−3177
428
−2795
−330
226
−1332
−1233
−3309
−74
−1
−213
−606
−1282
−618
−2
−272
−1514
−2102
−2−870
−303
−1118
−1594
−270
−1876
−377
−2294−652
−523
38
−1562
−1040
−629
−1240
632
−5
−1200
−920
−218
−2033
694
−719
−963
−542
−496
−17
−852
−1−215
−181
−1364
−1474
−572
−315
71
1083
−14
1269
−2165
−8
751
14
−1575
809
−8
−1100
−1692
−1178
−2298−611
−75
−1236
−2055
−238
−1537
−2281
−425−1139
−1032
176
150
−1637
−2621
277
271
64
412
−2399
−1918
−484
−2527
−1203
−2004
743
−1749
−1133
−48
−457−77
−142
−1769
−1472
−950
802
−9
324
−5−24
−554
−728
−200
−104
339
46
437
30
−206
−177
−2029
1656−408
−1175
789
−526
−177
1402
−369
−1248341
−1556
278
244
−1899
−455
120
−19
16
−27
−55
−680
−903
−1402
−638
731
−504
−53
94
770
−1−20
−59
−1258
−2682
−692
175
1017
−208
−2138
−696
−3058
−1
−1897
−3
−1820
84
−14
3
−1524
−1945
−66−748
−1648
−506
−1500
−640
−172
−4127
−1970−845
−1535
588
−302
−2109
−557
416
187
2
71
−1211
907
−1850
−2252
−2046
303
−4
−328
−1250
−941
−623−119
−139
−437
−274
−88
−406
−10
−26
1243
−177
−752
−2
−305
126
−7
−323
−37
125
−1355
147
−566−443
32
−795
−49
−760
−487
4
−1087302
−291
237
−57
−456
−320
−1035
6
0
68
−13
−517
−83
−128
180
−579
−505
−159
−536
−337
−180−396
−292
284
29
−349
−1375
32
−1177
26−253
63
−1516
9
−1102
4
9
−55
−32
−620
−2065
−316
−924−64
2
−2165
−1708
−1918
−2456
−518
205−542
−507
−289
−552
−21
−1840
−385
89
15
−64
−1947
−105
−2127
−585
−1623
−2147
114
−664
5
−497
−459−463
−388
380
62
−403
−1656
115
−660
−3−640
−331
−593
−4
−651
−56
6
−280
152
−392
−1020
−520
−891−585
−51
−467
−1026
−1523
−1581
−174
−328−210
12
22
−417
0
−1281
−1122
−419
4
−199
−1168
−218
−989
−169
−888
−980
−468
−596
39
−52
−712−12
−295
−305
−182
−821
−1101
−1685
573
−783−46
−49
−471
−385
−50
34
−923
350
−75
−534
−557
−89
−1181132
−203
−275
838
−1491
−499
−700
−7206
−234
−1202
−1287
35
617
100
−1528
6
−820
890
312
164
−1308
−1923
−926
−158
−91
−103
−2565
−290−1867
−1385
−3693
−3050
−3581
−932
−3626
−2382
−167018
−4286
−3395
−14
−2708
−4572
−2349
−3392
−4187
−1553
−3365
−2678
−495−1433
−5147
−143
−956
−1095
−3430
−1010
−2142−5309
−964
−3548
−5026
−1079
−3791
−3720
−3847
118
21
−2385
−785
−816
−4017
−4070
−2198
−4466
−1756
509
−1785
−1168−222
−73
−863
−2318
−760
−1613
110
−1175
585−52
−3
111
15
−1530
514
−131
930
14
−716
−1857
−47
−188−1496
121
−688
−1747
−805
−1144
−292
−881−1018
−225
−4
−3176
−425
−1397
−348
291
153
−117
−1679
−1555
−2542
−627
59
−803
−32
−277
−1146
IFNA1NR1D1
CRY1ARNTLNFIL3
DBPPER1
TNFNONO
BHLHE40PER2
FBXL21TEF
NR1D2NR1I3WDR5
CSNK1DCSNK2A1
AHRPER3
CLOCKALAS1
CSNK2A2PPP5C
CRY2PARP1NPAS2
PPP1CCCSNK2B
FBXL3SIRT1
ARNTL2RORB
CSE1LHLF
FBXW11RORA
BHLHE41CREB1
CSNK1EGSK3B
GNB2L1EP300PPARAPRKCARORC
CREBBPPPARG
BTRCPRKAA2PPP1CA
LIH
C
LUSC
PRAD
KIR
C
LUAD
THC
A
HN
SC
KIR
P
KIC
H
CO
AD
BLC
A
BRC
A
STAD
−5000 −2500 0 2500 5000
ARNTL
ARNTL2
CLOCK
CRY1
CRY2
NPAS2
NR1D1
NR1D2
PER1
PER2
PER3
RORA
RORB
RORC
ARNT
L
ARNT
L2
CLO
CK
CRY1
CRY2
NPAS
2
NR1D
1
NR1D
2
PER1
PER2
PER3
RORA
RORB
RORC
−0.8
−0.4
0.0
0.4
Cor
Coe
f
f.
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●● ●
●
●
●
●●
●
●
●
●
●
●●
●
●●●
●
●
●
●
●●
●
R = 0.079R = −0.47
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
● ●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●● ●
●
●
●
●●
●
●
●
●
●
●●
●
●● ●
●
●
●
●
●●
●
R = −0.28R = 0.46
●
●
●
●
●
●
●
●
●
● ●
●
●
●
●
●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●● ●
●
●
●
● ●
●
●
●
●
●
●●
●
●● ●
●
●
●
●
●●
●
R = −0.056R = −0.7
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●●
●
●
●
●●
●
●
●
●
●
●●
●
●● ●
●
●
●
●
●●
●
R = 0.38R = 0.58
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
● ●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●● ●
●
●
●
● ●
●
●
●
●
●
●●
●
●●●
●
●
●
●
●●
●
R = −0.05R = −0.54
●
●
●
●
●
●
●
●
●
● ●
●
●
●
●
●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●● ●
●
●
●
●●
●
●
●
●
●
●●
●
●● ●
●
●
●
●
●●
●
R = 0.00054R = 0.32
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●●
●
●
●
●●
●
●
●
●
●
●●
●
●● ●
●
●
●
●
●●
●
R = 0.13R = 0.53
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●●
●
●
●
● ●
●
●
●
●
●
●●
●
●●●
●
●
●
●
●●
●
R = 0.26R = 0.49
PER2 PER3 RORB RORC
ARNTL ARNTL2 NPAS2 PER1
0 5 10 0 5 10 0 5 10 0 5 10
9
10
11
12
9
10
11
12
Gene Expression
CRY
2 G
ene
Expr
essi
on
● ●Normal Tumor
A B
C
Number of positively correlated genes
0 4 8 12 16 20 24 280 4 8 12 16 20 24 28
CTCT
MCF10A MCF7
−2−1
01
2
Z−sc
ore
Collecting duct acid secretion
Wnt signaling pathway
Oxytocin signaling pathway
Vibrio cholerae infection
Epithelial cell signaling in Helicobacter pylori infection
TNF signaling pathway
Toll−like receptor signaling pathway
0 0.5 1 1.5 2−log10(p value)D
Figure S4. Related to Figure 4. Disruption and reprogramming of circadian rhythms in cancer. (A) The number of genes which positively correlated to clock genes (Pearson correlation coefficient ≤ -0.5 and FDR < 0.05, number in cell) decreased (blue) or increased (red) in tumor samples compared to paired normal samples for each clock gene in each cancer type. Pearson correlation is corrected by tumor purity in cancer samples. (B) Heatmap presents pairwise Pearson correlation coefficient (R) of core clock genes in tumor (left upper panel) and normal (right bottom panel) samples in KIRP. Red and blue frames indicate the correlation between CRY2 and other core clock genes. (C) Correlation between the transcriptional expression of CRY2 and other eight core clock genes in tumor (red) and normal (blue) samples in KIRP cancer type. (D) Heatmaps displaying the circadian oscillation pattern of genes predicted by JTK_CYCLE and MetaCycle::meta2d (P < 0.05) in MCF7 (right), and displaying oscillation pattern of these genes in MCF10A (left) with same gene order of MCF7. Red, high expression; blue, low expression. X-axis displayed time points after serum shock. (E) Gene ontology analysis for genes with newly established circadian rhythm in MCF7.
E
9
10
11
12
I II III IVStages
Gen
e Ex
pres
sion
Subtypes
Gen
e Ex
pres
sion
KIRC-CRY2 (FDR = 3.9 x 10-36）
A B
0 2000 4000 6000
0.0
0.2
0.4
0.6
0.8
1.0
Survival in days
p = 0.00045
0 1000 2000 30000.
00.
20.
40.
60.
81.
0Survival in days
HighLow
p = 1.4 x 10-5
Surv
ival
rate
Surv
ival
rate
KIRC-CRY2KIRP-CRY2C
ED
8.5
9.5
10.5
11.5
12.5
1 2 3 4
PRKCA TNF
NPAS2 NR1I3 PPARA
ARNTL2 CSNK2A2 NFIL3
TNBCLu
mALu
mBHer2
TNBCLu
mALu
mBHer2
TNBCLu
mALu
mBHer2
4
8
8
8
0
4
0
4
8
4
8
12
4
8
12
4
8
12
Gen
e E
xpre
ssio
n
PRKAA2 RORB RORC
FBXL3 NR1D1 PER2
BHLHE40 BTRC CRY2
TNBCLu
mALu
mBHer2
TNBCLu
mALu
mBHer2
TNBCLu
mALu
mBHer2
8
12
8
12
4
8
12
8
12
8
12
0
4
8
8
12
8
12
0
4
8
12
Gen
e E
xpre
ssio
n
KIRP-CRY2 (FDR = 0.0013)HighLow
Figure S5 Related to Figure 5. Individual cases for clock genes associated with patient survival, stage and subtype. (A) Association between CRY2 expression and overall survival (blue: low expression; red: high expression). (B and C) CRY2 shows differential expression in different tumor stages (B) and sub-types (C) in KIRP. (D and E) Expression levels for clock genes significantly upregulated and downregulated in TNBC compared to three other subtypes of breast cancer, respectively.
Num
ber o
f CAG
s
Cor
rela
tion
pairs
Negative PositiveCB
NR1D1FBXL21PPP5CPRKCAWDR5IFNA1
CSNK1DCSNK2A2
PER3FBXL3PER2
CSE1LNR1I3
TEFCSNK2A1
CLOCKALAS1
CREBBPGNB2L1
NPAS2PPP1CC
HLFDBP
RORCNR1D2NONOEP300BTRCPER1
CSNK2BSIRT1
PRKAA2PPARA
FBXW11CRY2
PPP1CAPARP1GSK3BRORBCRY1
CSNK1EPPARGCREB1ARNTL
BHLHE41AHR
RORABHLHE40
NFIL3ARNTL2
TNF
TNFR
SF4TG
FB1
CD276
ADORA2APDCD1
ICOSLG
HAVCR2CD4
CXCR4 IL2CTL
A4IL1
AIC
OSTN
FSF4
CCL2 IL6TN
FRSF9
PDCD1LG2
CD274
−10 0 10 20
Experimental evidence for protein-protein interaction
ChIP-seq evidence for interaction
The number of cancer types
Negative Positive
0
50
100
150
LUSC
CHO
LO
VBL
CACE
SCBR
CALU
AD UCS
STAD
HNSC
ESCA
UCEC
LIHC
SARC AC
CCO
ADG
BMDL
BCKI
RPLG
GPC
PGKI
RCPR
ADRE
ADTH
CAPA
ADM
ESO
SKCM
KICH
UVM
THYM
TGCT
0
1000
2000
LUSC
CH
OL
OV
LUAD
CES
CU
CS
BLC
AES
CA
BRC
AST
ADH
NSC
SAR
CAC
CLI
HC
CO
ADU
CEC
PCPG
MES
OG
BMR
EAD
KIR
CKI
RP
SKC
MLG
GPA
ADKI
CH
PRAD
DLB
CTH
CA
TGC
TU
VMTH
YM
● ●●● ● ● ● ● ● ●●●●●●●● ● ● ●●● ● ● ●●●●●● ● ●
ACC
BLC
A
BRC
A
CES
C
CH
OL
CO
AD
DLB
C
ESC
A
GBM
HN
SC
KIC
H
KIR
C
KIR
P
LGG
LIH
C
LUAD
LUSC
MES
O OV
PAAD
PCPG
PRAD
REA
D
SAR
C
SKC
M
STAD
TGC
T
THC
A
THYM
UC
EC UC
S
UVM
FDR ● ● ● ●0.05 10−5 10−10 < 10−15
−1 −0.5 0 0.5 1Cor Coeff. R
A
D
Figure S6. Related to Figure 6. Co-expression of clinically actionable genes and clock genes varied across cancer types. (A) Clock genes correlated to targeted genes for immunotherapy; blue: negative correlation; red: positive correlation; color scale: the number of cancer types with negative or positive correlation between clock genes and CAGs. If the number of cancer types is less than three, the fill color of cell is white. Bold boxes: protein-protein interactions from BioGRID and HPRD. X marks: ChIP-seq evidence for interaction. (B) Number of pairs of CAGs which correlated to clock genes across cancer types. (C) Number of correlation pairs between transcriptional expression of CAGs and clock genes across cancer type (blue: negative correlation; red: positive correlation). (D) The Pearson correlation between transcriptional expression of CLOCK and NR1D2 across 32 cancer types. The color inten-sity indicates the Pearson correlation coefficient (R), the point size indicates FDR. Black circles show the correlation with statistical significance (|R| > 0.3, FDR < 0.05).
A C
B
−10−5 0 5 10zscore
E
030
6090
PAR
P1C
REB
1PP
P1C
CTN
FSI
RT1
EP30
0N
ON
OPE
R2
RO
RB
CR
EBBP
PPP5
CC
RY2
GN
B2L1
FBXL
3C
SNK2
A2C
SNK2
A1D
BPC
SNK1
ER
OR
CW
DR
5PE
R1
NR
1I3
PPP1
CA
BTR
CAL
AS1
PPAR
APE
R3
FBXW
11G
SK3B
NFI
L3R
OR
ATE
FC
SE1L
BHLH
E41
ARN
TL2
CRY
1N
PAS2
NR
1D2
CLO
CK
CSN
K1D
PRKA
A2BH
LHE4
0PP
ARG
AHR
Com
poun
ds C
ount Positive Cor Negative CorGDSC
P
●● ● ●● ●● ●●● ● ● ●● ●●● ●● ● ●● ●●● ● ●●●●● ●● ●● ●●● ● ●● ●● ● ● ●● ● ● ●● ● ●●●●● ●● ●●● ●● ●● ● ● ●●●● ●●● ●● ●● ●● ●● ● ● ● ●● ●●●●●● ● ● ●● ● ●●●● ●● ●● ●●● ● ● ●● ●● ●● ●●● ●●● ●● ●●●● ● ●●
●●●
● ●● ● ●● ●● ●● ● ●●● ●● ●● ●●● ● ●● ●● ●● ●● ●● ●●●● ●● ●●● ●● ●●●
● ●●● ●●● ●● ●
● ●● ●
●● ● ●● ●● ● ● ●● ●●●● ●● ● ●●
●● ● ●● ●●● ●● ●● ● ●● ●●●●● ●●● ●● ●●● ● ●● ● ●● ● ●●● ●● ●● ●● ●● ●● ●● ●●●● ● ●●● ●● ●●●● ● ●●● ● ●● ● ●●● ●●● ●●● ●● ●● ●● ●●
● ●● ● ●● ●●● ●●● ● ●●● ●● ● ●●● ●● ● ●● ●●● ● ●●●●● ●● ●● ● ●●● ● ●● ●●● ● ● ●● ●●● ● ● ●● ● ●●●●● ●● ● ●●●● ● ●●● ●● ●● ● ● ●●●● ●●●●● ●● ●● ●● ●● ● ●● ● ●● ●●●●●● ● ● ●●● ● ●●●●● ●● ●● ● ●●● ●● ● ●● ●● ●● ●● ●●● ●● ●●● ●●● ●●●● ● ●●
● ●● ● ●● ●● ●●● ● ● ●● ● ●●● ●● ● ●● ●●● ● ●●●●● ●● ●● ● ●●● ● ●● ●● ● ●● ●●● ● ●● ● ●●●●● ●● ● ●●●● ●● ●● ● ● ● ●●● ● ●● ●● ●● ●● ● ●● ●●●●● ●●● ● ●●●●● ●● ●● ●●● ● ● ●●● ●● ● ●●● ●● ●●● ●● ●● ● ●●
●● ● ●● ●●● ● ●●● ●●●● ●● ● ●●● ●●●● ● ●● ●●● ●● ●● ● ●● ●● ● ● ●● ● ●●●●● ●● ● ●●●● ●● ●● ●● ● ● ●● ●●● ●● ●● ●●● ● ● ●●●● ● ●●●● ●● ●● ● ● ●●●● ● ●● ● ●● ●● ●●● ● ●●
●●● ● ●● ● ●● ● ● ●● ●● ●●● ● ● ●● ●● ●●● ●● ●●●
●
● ● ● ●●● ●●●● ● ●● ●●● ● ● ●●● ● ●● ● ●● ●● ●●●● ●● ●● ●● ●● ●● ●●●● ●● ●●● ●● ● ●● ●●●●● ●●
●● ● ● ●● ●● ●●●●● ●● ● ● ●● ●●●●● ●● ●● ●● ●●● ● ●● ●● ●● ● ●●●● ●● ● ●●● ●●● ●● ●● ●●●●● ●●● ● ● ●●●● ● ●● ●●●● ● ●●● ●●● ● ●●●● ●● ●● ●●
● ●● ●● ● ●●●● ●● ● ●● ●● ●●● ●● ●● ●● ● ●●● ●● ●● ●● ●● ●●●●
● ●● ●●● ● ●● ●●●● ●● ●●●● ●● ●● ●● ●●● ● ●●●● ●●●●●
● ●● ● ● ●●● ●● ●●● ● ●●●● ● ●●●● ● ●●●●● ●● ● ● ● ●● ● ●●●●● ●● ● ●● ●● ●● ● ●● ●●● ●● ●●●● ● ● ●● ●●●● ● ●● ● ●●●● ●● ● ●●● ● ●●● ●●● ● ●● ●● ●●● ● ●●
●● ● ●● ●● ●●● ● ●●● ●● ●● ●● ●●● ● ●●●●● ●● ●● ●●● ●● ●● ●● ●●● ● ● ●● ● ●●●●● ●● ● ●●●● ● ●●● ●● ● ● ● ●● ●●●● ●● ●● ●● ●● ●● ● ●● ●●●● ● ● ●●●●● ●● ●●● ● ● ●● ●● ● ●●● ● ●● ●●● ●●● ● ●●
●● ● ●●●● ●●● ● ●● ●●●●● ●● ●● ●● ●● ●● ●● ●● ● ●●●●● ● ●●● ● ●● ● ●●● ●● ●●● ● ●●● ● ●●● ●●●● ● ●● ●●● ●● ● ●● ●●● ●●
●
●●
● ●● ● ●● ●●● ●●● ● ●●● ●● ● ●●● ●● ● ●● ●●● ● ●●●●● ●● ●● ● ●●● ● ●● ● ●●● ● ● ●● ●●● ● ● ●● ● ●●●●● ●● ● ●●●● ● ●●● ●● ●●● ● ● ●●●● ●●●●● ●● ●● ●● ●● ● ● ● ●● ●●●●●● ● ● ●●● ● ●●●● ●● ●● ●●● ●● ● ●●● ●● ●● ●●● ●● ●●● ●●● ●●● ● ●●
● ●● ● ● ●● ●● ●●● ●●● ●● ● ●● ● ●●●●● ●● ●●●● ●● ●● ●● ● ●●●● ●● ● ●●● ●● ●● ●● ● ●●● ●●● ●●● ●●● ● ●● ●●●● ●● ●●● ●● ● ●●● ● ● ●●●● ●●●● ●● ●●●● ● ●●
●● ●● ●● ● ●● ● ● ●● ● ●●●● ●●● ● ●● ● ● ●● ●●●● ●● ●● ●● ●● ● ●● ●●●● ● ●●●● ● ● ●● ●● ● ●●● ● ●●● ●●●●
●● ●● ●● ●●●● ●● ● ●●●● ● ●● ●● ●●●● ● ● ●● ● ●●●●● ● ●●● ● ●● ● ●●● ●● ●●● ●● ● ● ●●● ● ●●● ●●●● ● ● ●●● ● ● ●●● ● ●● ●● ●● ●●
● ●●● ●●●● ●● ●● ● ●●● ● ●● ●●● ●● ●●
● ●● ● ●● ●●● ●●● ● ●●● ●● ● ●●● ●● ● ●● ●●● ● ●●●●● ●● ●● ● ●●● ● ●● ● ●●● ● ● ●● ●●● ● ● ●● ● ●●●●● ●● ● ●●●● ● ●●● ●● ●●● ● ● ●●●● ●●●●● ●● ●● ●● ●● ● ● ● ●● ●●●●●● ● ● ●●● ● ●●●●● ●● ●● ● ●●● ●● ● ●● ●● ●● ●● ●●● ●● ●●● ●●● ●●●● ● ●●
●● ●● ●●● ●● ● ●●●●● ●● ●●● ●●● ●●●● ●●● ●● ● ●● ●● ●● ● ●● ●●●● ● ●●● ● ● ● ● ●●● ● ●●●●●
● ●● ● ●●● ●●● ● ●● ●●● ● ● ●● ●●●●● ●● ●● ●● ●● ● ●● ● ●● ●●● ●● ● ●●●●● ● ● ●●●● ●●● ● ●● ● ●● ●● ●● ●●● ●● ●●●●● ●●● ●●● ●● ● ●● ●● ●● ●● ●●● ● ●● ●●● ●● ●●
●● ●● ●
●● ●
●●●● ●● ●●● ● ●●● ● ●●●●● ●●●●● ●● ● ●● ●●● ● ●●● ●● ● ●● ●● ●● ● ● ●● ●● ●● ● ●●● ●● ● ● ● ● ●●● ●● ●●●
●● ● ● ●●● ●●● ● ●●● ●● ● ●●● ●● ● ●● ●●● ● ●●●●● ●● ●● ● ●●● ● ●● ● ●●● ● ● ●● ●●● ● ● ●● ● ●●●●● ●● ● ●●●● ● ●●● ●● ●●● ● ● ●●●● ●●●●● ●● ●● ●● ●● ● ● ● ●● ●●●●●● ● ● ●●● ● ●●● ●● ●● ● ●●● ●● ● ●● ●● ●● ●● ●●● ●● ●●● ●●● ●●●● ● ●●
● ●● ● ●● ●● ● ● ●●● ●● ● ● ●●● ● ●●●● ● ●●● ●● ●● ● ● ● ●● ●●●●● ●● ●●● ●● ●● ●● ●●● ●●● ●●● ● ●●●●●● ● ●●● ● ●●● ●● ●● ●● ●●● ●● ●●● ●● ●● ●●● ●●
● ● ●● ●●● ● ●●●●● ●● ●●● ●● ●●● ●● ● ●● ●●● ●●● ● ● ●●● ●●● ●● ●● ●●● ●● ● ● ●●●● ● ●●●●● ●● ●●● ●● ● ●● ●●●●●
● ●● ● ●● ●● ●● ●● ● ●●● ●● ● ●●● ●● ● ●●● ●● ●●
●●● ● ●● ●● ●● ●●●● ●● ● ●● ●● ● ●● ●● ● ● ●●●●●
●
●
●● ● ●● ●●● ●●● ● ●● ●● ● ●●● ● ● ●● ●●● ● ●●●●● ●● ●● ● ●●● ● ●● ●● ● ● ●● ●●● ● ● ●● ● ●●●●● ●● ● ●●●● ● ●●● ●● ●● ● ● ●●●● ●●●● ●● ●● ●● ●● ● ●● ● ●● ●●●●●● ● ● ●●● ● ●●●●● ●● ●● ●●● ●● ● ●●● ●● ●● ●●● ●● ●●● ●● ●●● ● ●●
● ●●● ●●
● ●● ●● ●● ●●●● ● ● ●●●● ●●● ●● ●● ● ●● ●●●●● ●● ●● ●● ●● ● ● ●● ●●● ●●● ●● ● ● ●●●● ● ● ●● ●●● ●● ● ●● ● ●●● ● ●● ●●●● ●●
●● ● ●● ●● ●●● ● ●● ●●●●● ●●● ● ●● ●●●● ●● ●● ● ●●● ● ●●● ● ●● ●● ● ●● ●● ●● ● ●●●● ● ●●●● ● ●● ●●●● ● ●● ●● ●● ●●●●
PARP1CREB1NONO
PPP1CCSIRT1
CREBBPEP300CRY2PER2DBP
PPP5CCSNK2A1
TNFGNB2L1
WDR5CSNK1E
PER1CSNK2A2CSNK2B
RORANR1I3BTRC
ALAS1PPARANFIL3
GSK3BRORBRORCCRY1
FBXW11FBXL21FBXL3
HLFIFNA1
ARNTLPPP1CACSNK1D
BHLHE41PER3
TEFBHLHE40
CSE1LPRKCA
ARNTL2NR1D1PPARG
PRKAA2NR1D2CLOCKNPAS2
AHR
PX−1
2de
cita
bine
cyta
rabi
ne h
ydro
chlo
ride
YK 4
−279
vinc
ristin
etr
iazo
loth
iadi
azin
eis
oevo
diam
ine
LY−2
1832
40G
SK46
1364
etop
osid
edo
xoru
bici
nSR
−II−
138A
parb
enda
zole
ML3
11M
erck
60cl
ofar
abin
ePH
A−7
9388
7K
X2−3
91ci
clop
irox
BR
D−K
6645
3893
BI−
2536
topo
teca
nSB
−743
921
rigos
ertib
PL−D
IN
VP−2
31B
RD
−K70
5115
74B
RD
−K61
1665
97ba
rase
rtib
alis
ertib
indi
sula
mI−
BET
151
GSK
5257
62A
CH
M−1
BR
D−K
3422
2889
SB−2
2500
2pi
perlo
ngum
ine
narc
icla
sine
JQ−1
FQI−
2C
R−1
−31B
CD
−437
apic
idin
pano
bino
stat
pacl
itaxe
lna
kite
rpio
sin
KW
−244
9ch
lora
mbu
cil
cera
nib−
2vo
rinos
tat
mito
myc
inm
anum
ycin
Age
mci
tabi
neax
itini
bpe
vone
dist
atN
SC95
397
MK
−177
5A
ZD77
623−
Cl−
AH
PCte
nipo
side
PRIM
A−1
KPT
185
GW
−843
682X
entin
osta
tSN
X−21
12se
rdem
etan
NVP
−BSK
805
NSC
4830
0LR
RK
2−IN
−1flu
orou
raci
lda
carb
azin
eC
ompo
und
23 c
itrat
ece
rule
nin
BR
D−K
8018
3349
BIX
−012
94be
linos
tat
tipifa
rnib
−P1
obat
ocla
xne
uron
al d
iffer
entia
tion
indu
cer I
IIle
ptom
ycin
BIS
OX
GW
−405
833
curc
umin
CC
T036
477
BR
D−A
9437
7914
STF−
31om
acet
axin
e m
epes
ucci
nate
criz
otin
ibC
OL−
3B
RD
−K66
5322
83tr
etin
oin
TPC
A−1
tivan
tinib
siro
limus
phlo
retin
PAC
−1nu
tlin−
3ne
cros
ulfo
nam
ide
MST
−312
BR
D18
12TG
−101
348
SN−3
8PF
−573
228
NSC
6328
39K
U−6
0019
KU
006
0648
GM
X−17
78cu
curb
itaci
n I
Com
poun
d 7d
−cis
CAY
1061
8B
RD
−K35
6044
18ta
cedi
nalin
eSN
S−03
2PF
−184
ouab
ain
olap
arib
NSC
1963
0m
omel
otin
ibva
ldec
oxib
TW−3
7tip
ifarn
ib−P
2SU
1127
4so
tras
taur
inSC
H−7
9797
RIT
API
K−9
3pi
fithr
in−m
uPI
−103
PF−3
7583
09O
SI−9
30M
L239
MK
−220
6go
ssyp
olfin
golim
odep
igal
loca
tech
in−3
−mon
ogal
late
WP1
130
trip
tolid
eSt
emR
egen
in 1
SMER
−3ru
xolit
inib
ML2
10M
GC
D−2
65lin
ifani
bdo
ceta
xel
dexa
met
haso
neda
porin
adB
RD
−K92
8560
60A
BT−
737
RG
−108
olig
omyc
in A
NVP
−TA
E684
MLN
2238
ML0
31m
etho
trex
ate
eras
tindi
naci
clib
BR
D−K
4159
7374
BR
D−K
2653
1177
bort
ezom
ibB
MS−
3455
41ba
rdox
olon
e m
ethy
lA
Z−31
46AT
7867
Pvalue ● ● ● ●0.05 10−5 10−10 < 10−15
BHLH
E40
AHR
NPA
S2C
SNK1
DPP
ARG
CSE
1LC
RY1
CLO
CK
PRKA
A2N
R1D
2TN
FPE
R2
EP30
0PA
RP1
CR
EB1
PPP1
CC
NO
NO
RO
RB
SIR
T1C
REB
BP
BHLHE40AHRNPAS2CSNK1DPPARGCSE1LCRY1CLOCKPRKAA2NR1D2TNFPER2EP300PARP1CREB1PPP1CCNONORORBSIRT1CREBBP
−0.5 0 0.5Cor Coeff R
−20 −10 0 10 20
0.00
0.05
0.10
0.15
z−scored correlation strength
Prob
alilit
y de
nsity
est
imat
e
D
Random pairs
Targeted pairs
Figure S7. Related to Figure 7. Correlation between clock gene expression and drug sensitivity. (A) Distribution of z-scored Pearson correlation coefficients between 128 annotated small molecule–target pairs (111 compounds and 83 target genes, green) across all cancer cell lines compared to random sampling of correlation coefficients (black) in GDSC. Dashed line represents two-tailed Bonferroni-corrected significance (|z| = 3.89). (B) and (D) The number of compounds with positive (red) and negative (blue) correlation of expression levels of clock related genes and drug sensitivity in GDSC and CTRP, respectively. (C) Hierarchi-cal clustering of Pearson correlation coefficient for top 10 genes of same correlation tendency with drug sen-sitivity in two groups (left and right of top 10 genes in Figure 6A, respectively). (E) Correlation between drug sensitivity and clock genes in at least 10 clock genes (green: negative correlation; magenta: positive correla-tion; size: p-value) in CTRP .
010
020
0C
ompo
unds
Cou
nt Positive Cor Negative CorCTRP
PAR
P1C
REB
1N
ON
OPP
P1C
CSI
RT1
CR
EBBP
EP30
0PE
R2
CRY
2PP
P5C
DBP
CSN
K2A1
GN
B2L1
TNF
WD
R5
CSN
K1E
PER
1C
SNK2
A2C
SNK2
BR
OR
AN
R1I
3BT
RC
ALAS
1N
FIL3
P PAR
AR
OR
BAR
NTL
CRY
1G
SK3B HLF
RO
RC
CSN
K1D
FBXW
11BH
LHE4
1PE
R3
TEF
BHLH
E40
CSE
1LPR
KCA
ARN
TL2
NR
1D1
PAR
GPR
KAA2
NR
1D2
CLO
CK
NPA
S2AH
R
Cancer type Abbreviation Name
# of Tumor Samples
# of Normal Samples
Tumor/Normal Pair
Adrenocortical Carcinoma ACC 79 0 No Bladder Urothelial Carcinoma BLCA 408 19 Yes Breast Invasive Carcinoma BRCA 1104 114 Yes Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma CESC 307 0 No Cholangiocarcinoma CHOL 36 0 No Colon Adenocarcinoma COAD 288 26 Yes Lymphoid Neoplasm Diffuse Large B-cell Lymphoma DLBC 48 0 No Esophageal Carcinoma ESCA 185 11 Yes Glioblastoma Multiforme GBM 169 0 No Head and Neck squamous Cell Carcinoma HNSC 522 43 Yes Kidney Chromophobe KICH 66 25 Yes Kidney Renal Clear Cell Carcinoma KIRC 534 72 Yes Kidney Renal Papillary Cell Carcinoma KIRP 291 32 Yes Brain Lower Grade Glioma LGG 534 0 No Liver Hepatocellular Carcinoma LIHC 374 50 Yes Lung Adenocarcinoma LUAD 517 58 Yes Lung Cquamous Cell Carcinoma LUSC 503 51 Yes Mesothelioma MESO 87 0 No Ovarian Serous Cystadenocarcinoma OV 309 0 No Pancreatic Adenocarcinoma PAAD 179 0 No Pheochromocytoma and Paraganglioma PCPG 184 0 No Prostate Adenocarcinoma PRAD 498 52 Yes Rectum Adenocarcinoma READ 95 0 No Sarcoma SARC 263 0 No Skin Cutaneous Melanoma SKCM 473 0 No Stomach Adenocarcinoma STAD 415 32 Yes Testicular Germ Cell Tumors TGCT 156 0 No Thyroid Carcinoma THCA 513 59 Yes Thymoma THYM 120 0 No Uterine Corpus Endometrial Carcinoma UCEC 177 0 No Uterine Carcinosarcoma UCS 57 0 No Uveal Melanoma UVM 80 0 No
Supplementary tables
Table S1. Related to STAR Methods. Number of tumor and normal samples in each cancer type