Supplementary Information
Suppl. Table 1. List of 310 cell cycle arrest genes used in Figure 1A and co-expression
analysis.
Probe ID
NM_018518
NM_002192
NM_001924
NM_001077181
NM_001923
NM_004354
NM_002191
Gene
SYMBLE
Mcm10
INHBA
GADD45A
CDC14B
DDB1
CCNG2
inhA
NM_002675
NM_002393
NM_000368
NM_002392
NM_003246
NM_005343
NM_000785
NM_002873
PML
MDM4
TSC1
mdm2
Thbs1
hras
CYP27B1
RAD17
NM_006191
NM_002388
NM_001136197
NM_015986
NM_006739
PA2G4
MCM3
FZR1
CRLF3
Mcm5
NM_000882
NM_000986
NM_001135599
NM_006478
NM_001723
NM_003341
NM_001003786
NM_016448
NM_000619
NM_001130831
NM_022836
NM_003333
IL12A
rpl24
TGFB2
GAS2L1
DST
UBE2E1
STRADA
dtl
IFNG
gas7
DCLRE1B
uba52
Gene Name
minichromosome maintenance complex component 10
inhibin, beta A
growth arrest and DNA-damage-inducible, alpha
CDC14 cell division cycle 14 homolog B (S. cerevisiae)
damage-specific DNA binding protein 1, 127kDa
cyclin G2
inhibin, alpha
promyelocytic leukemia; similar to promyelocytic leukemia protein isoform
1
Mdm4 p53 binding protein homolog (mouse)
tuberous sclerosis 1
Mdm2 p53 binding protein homolog (mouse)
thrombospondin 1
v-Ha-ras Harvey rat sarcoma viral oncogene homolog
cytochrome P450, family 27, subfamily B, polypeptide 1
RAD17 homolog (S. pombe)
proliferation-associated 2G4, 38kDa; proliferation-associated 2G4
pseudogene 4
minichromosome maintenance complex component 3
fizzy/cell division cycle 20 related 1 (Drosophila)
cytokine receptor-like factor 3
minichromosome maintenance complex component 5
interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic
lymphocyte maturation factor 1, p35)
ribosomal protein L24; ribosomal protein L24 pseudogene 6
transforming growth factor, beta 2
growth arrest-specific 2 like 1
dystonin
ubiquitin-conjugating enzyme E2E 1 (UBC4/5 homolog, yeast)
STE20-related kinase adaptor alpha
denticleless homolog (Drosophila)
interferon, gamma
growth arrest-specific 7
DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)
ubiquitin A-52 residue ribosomal protein fusion product 1
NM_003338
NM_001130112
NM_001800
NM_002799
NM_002798
NM_002796
NM_002795
NM_002467
NM_002794
NM_000389
NM_005973
NM_018124
NM_002894
UBE2D1
RFC5
CDKN2D
psmb7
PSMB6
PSMB4
PSMB3
MYC
psmb2
CDKN1A
PRCC
RFWD3
RBBP8
XM_940791
NM_000251
NM_001122631
NM_006716
NM_002788
NM_002787
NM_001145769
NM_002786
NM_001031716
NM_001161725
NM_016426
NM_006306
NM_004343
NM_004701
NM_016628
NM_004336
NM_005789
NM_002790
NM_016399
NM_002791
NM_002485
NM_004507
NM_002792
NM_002793
NM_001137559
NM_016290
NM_000321
NM_100486
NM_003496
NM_016237
ATM
Msh2
CDKN1C
Dbf4
Psma3
psmA2
XPC
PSMA1
OBFC2A
PPP2R5C
GTSE1
Smc1a
CALR
CCNB2
WAC
BUB1
PSME3
psma5
TRIAP1
Psma6
NBN
HUS1
PSMA7
psmb1
ANAPC5
uimc1
RB1
WAC
TRRAP
ANAPC5
ubiquitin-conjugating enzyme E2D 1 (UBC4/5 homolog, yeast)
replication factor C (activator 1) 5, 36.5kDa
cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)
proteasome (prosome, macropain) subunit, beta type, 7
proteasome (prosome, macropain) subunit, beta type, 6
proteasome (prosome, macropain) subunit, beta type, 4
proteasome (prosome, macropain) subunit, beta type, 3
v-myc myelocytomatosis viral oncogene homolog (avian)
proteasome (prosome, macropain) subunit, beta type, 2
cyclin-dependent kinase inhibitor 1A (p21, Cip1)
papillary renal cell carcinoma (translocation-associated)
ring finger and WD repeat domain 3
retinoblastoma binding protein 8
similar to Serine-protein kinase ATM (Ataxia telangiectasia mutated) (A-T,
mutated); ataxia telangiectasia mutated
mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)
cyclin-dependent kinase inhibitor 1C (p57, Kip2)
DBF4 homolog (S. cerevisiae)
proteasome (prosome, macropain) subunit, alpha type, 3
proteasome (prosome, macropain) subunit, alpha type, 2
xeroderma pigmentosum, complementation group C
proteasome (prosome, macropain) subunit, alpha type, 1
oligonucleotide/oligosaccharide-binding fold containing 2A
protein phosphatase 2, regulatory subunit B', gamma isoform
G-2 and S-phase expressed 1
structural maintenance of chromosomes 1A
calreticulin
cyclin B2
WW domain containing adaptor with coiled-coil
budding uninhibited by benzimidazoles 1 homolog (yeast)
proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki)
proteasome (prosome, macropain) subunit, alpha type, 5
TP53 regulated inhibitor of apoptosis 1
proteasome (prosome, macropain) subunit, alpha type, 6
nibrin
HUS1 checkpoint homolog (S. pombe)
proteasome (prosome, macropain) subunit, alpha type, 7
proteasome (prosome, macropain) subunit, beta type, 1
anaphase promoting complex subunit 5
ubiquitin interaction motif containing 1
retinoblastoma 1
WW domain containing adaptor with coiled-coil
transformation/transcription domain-associated protein
anaphase promoting complex subunit 5
NM_000546
NM_001145102
NM_000548
NM_003106
NM_012090
NM_014814
NM_005197
NM_001003690
NM_001005413
NM_005192
NM_001146003
tp53
SMAD3
TSC2
SOX2
MACF1
PSMD6
foxn3
Mad2l1bp
ZWINT
CDKN3
Nek11
NM_000122
NM_001211
NM_004725
NM_004724
NM_004629
NM_014909
NM_021953
NM_001623
NM_001789
NM_013347
NM_001786
NM_003884
NM_000038
NM_001166239
NM_001127582
NM_001790
NM_001105540
NM_001161344
NM_006568
NM_005399
NM_002358
NM_003478
NM_014708
NM_033379
NM_053056
NM_003223
NM_022809
NM_002758
NM_000660
NM_001080951
NM_002755
ercc3
BUB1B
Bub3
ZW10
Fancg
Vash1
FOXM1
Aif1
CDC25A
RPA4
Cdk1
KAT2B
APC
Cgref1
Ing4
CDC25C
DGKZ
CHFR
cgrrf1
PRKAB2
Mad2l1
CUL5
KNTC1
Cdk1
CCND1
TFAP4
CDC25C
map2k6
TGFB1
PLAGL1
MAP2K1
tumor protein p53
SMAD family member 3
tuberous sclerosis 2
SRY (sex determining region Y)-box 2
microtubule-actin crosslinking factor 1
proteasome (prosome, macropain) 26S subunit, non-ATPase, 6
forkhead box N3
MAD2L1 binding protein
ZW10 interactor
cyclin-dependent kinase inhibitor 3
NIMA (never in mitosis gene a)- related kinase 11
excision repair cross-complementing rodent repair deficiency,
complementation group 3 (xeroderma pigmentosum group B
complementing)
budding uninhibited by benzimidazoles 1 homolog beta (yeast)
budding uninhibited by benzimidazoles 3 homolog (yeast)
ZW10, kinetochore associated, homolog (Drosophila)
Fanconi anemia, complementation group G
vasohibin 1
forkhead box M1
allograft inflammatory factor 1
cell division cycle 25 homolog A (S. pombe)
replication protein A4, 34kDa
cell division cycle 2, G1 to S and G2 to M
K(lysine) acetyltransferase 2B
adenomatous polyposis coli
cell growth regulator with EF-hand domain 1
inhibitor of growth family, member 4
cell division cycle 25 homolog C (S. pombe)
diacylglycerol kinase, zeta 104kDa
checkpoint with forkhead and ring finger domains
cell growth regulator with ring finger domain 1
protein kinase, AMP-activated, beta 2 non-catalytic subunit
MAD2 mitotic arrest deficient-like 1 (yeast)
cullin 5
kinetochore associated 1
cell division cycle 2, G1 to S and G2 to M
cyclin D1
transcription factor AP-4 (activating enhancer binding protein 4)
cell division cycle 25 homolog C (S. pombe)
mitogen-activated protein kinase kinase 6
transforming growth factor, beta 1
pleiomorphic adenoma gene-like 1
mitogen-activated protein kinase kinase 1
NM_001798
Cdk2
NM_177951
NM_006263
NM_001079670
NM_178587
NM_001018055
NM_001114122
NM_001114121
NM_015920
NM_001237
NM_006559
NM_004899
NM_181803
PPM1A
PSME1
CAB39L
PPP2R5C
BRCC3
CHEK1
CHEK1
Rps27l
CCNA2
Khdrbs1
BRE
UBE2C
NM_003218
NM_015548
NM_025180
NM_004749
NM_021930
NM_001130851
NM_013239
NM_006253
NM_007019
NM_006251
NM_001130725
NM_006252
NM_001130849
NM_181800
NM_001255
NM_001254
NM_057749
NM_001256
NM_206907
NM_199191
NM_152902
NM_023015
NM_001143976
NM_005915
NM_000311
NM_005916
NM_000076
NM_001164
NM_015517
TERF1
DST
CEP63
TBRG4
rint1
CDKN3
PPP2R3B
PRKAB1
UBE2C
PRKAA1
PSMB5
prkaa2
cab39
UBE2C
cdc20
cdc6
Ccne2
cdc27
PRKAA1
BRE
TIPRL
INTS3
wee1
MCM6
PRNP
MCM7
CDKN1C
APBB1
hinfp
cyclin-dependent kinase 2
protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha
isoform
proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)
calcium binding protein 39-like
protein phosphatase 2, regulatory subunit B', gamma isoform
BRCA1/BRCA2-containing complex, subunit 3
CHK1 checkpoint homolog (S. pombe)
CHK1 checkpoint homolog (S. pombe)
ribosomal protein S27-like
cyclin A2
KH domain containing, RNA binding, signal transduction associated 1
brain and reproductive organ-expressed (TNFRSF1A modulator)
ubiquitin-conjugating enzyme E2C
similar to telomeric repeat binding factor (NIMA-interacting) 1; telomeric
repeat binding factor (NIMA-interacting) 1; telomeric repeat binding factor
(NIMA-interacting) 1 pseudogene
dystonin
centrosomal protein 63kDa
transforming growth factor beta regulator 4
RAD50 interactor 1
cyclin-dependent kinase inhibitor 3
protein phosphatase 2 (formerly 2A), regulatory subunit B'', beta
protein kinase, AMP-activated, beta 1 non-catalytic subunit
ubiquitin-conjugating enzyme E2C
protein kinase, AMP-activated, alpha 1 catalytic subunit
proteasome (prosome, macropain) subunit, beta type, 5
protein kinase, AMP-activated, alpha 2 catalytic subunit
calcium binding protein 39
ubiquitin-conjugating enzyme E2C
cell division cycle 20 homolog (S. cerevisiae)
cell division cycle 6 homolog (S. cerevisiae)
cyclin E2
cell division cycle 27 homolog (S. cerevisiae)
protein kinase, AMP-activated, alpha 1 catalytic subunit
brain and reproductive organ-expressed (TNFRSF1A modulator)
TIP41, TOR signaling pathway regulator-like (S. cerevisiae)
integrator complex subunit 3
WEE1 homolog (S. pombe)
minichromosome maintenance complex component 6
prion protein
minichromosome maintenance complex component 7
cyclin-dependent kinase inhibitor 1C (p57, Kip2)
amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)
histone H4 transcription factor
NM_021009
UBC
NM_021003
NM_001262
NM_001040633
NM_004584
PPM1A
CDKN2C
PRKAG2
RAD9A
NM_004159
NM_033266
NM_005914
NM_006023
NM_001134419
NM_001012270
NM_012257
NM_001012271
NM_002105
NM_001018159
NM_005146
NM_001168
NM_002914
NM_016343
NM_002915
NM_017975
NM_002916
NM_000077
NM_052827
NM_001130442
NM_002853
NM_001007793
NM_001078645
NM_002415
NM_024408
psmb8
ern2
MCM4
Cdc123
CDC7
BIRC5
HBP1
BIRC5
H2afx
Nae1
sart1
BIRC5
RFC2
CENPF
RFC3
ZWILCH
RfC4
CDKN2A
Cdk2
hras
RAD1
Bub3
CDC16
MIF
Notch2
NM_000400
NM_001114091
NM_000465
NM_019845
NM_001008895
ercc2
cdc27
BARD1
RPRM
cul4a
NM_006503
NM_001145097
NM_203292
NM_001098424
NM_001166691
psmc4
Skil
RBBP8
DLG1
ttk
ubiquitin C
protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha
isoform
cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)
protein kinase, AMP-activated, gamma 2 non-catalytic subunit
RAD9 homolog A (S. pombe)
proteasome (prosome, macropain) subunit, beta type, 8 (large
multifunctional peptidase 7)
endoplasmic reticulum to nucleus signaling 2
minichromosome maintenance complex component 4
cell division cycle 123 homolog (S. cerevisiae)
cell division cycle 7 homolog (S. cerevisiae)
baculoviral IAP repeat-containing 5
HMG-box transcription factor 1
baculoviral IAP repeat-containing 5
H2A histone family, member X
NEDD8 activating enzyme E1 subunit 1
squamous cell carcinoma antigen recognized by T cells
baculoviral IAP repeat-containing 5
replication factor C (activator 1) 2, 40kDa
centromere protein F, 350/400ka (mitosin)
replication factor C (activator 1) 3, 38kDa
Zwilch, kinetochore associated, homolog (Drosophila)
replication factor C (activator 1) 4, 37kDa
cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)
cyclin-dependent kinase 2
v-Ha-ras Harvey rat sarcoma viral oncogene homolog
RAD1 homolog (S. pombe)
budding uninhibited by benzimidazoles 3 homolog (yeast)
cell division cycle 16 homolog (S. cerevisiae)
macrophage migration inhibitory factor (glycosylation-inhibiting factor)
Notch homolog 2 (Drosophila)
excision repair cross-complementing rodent repair deficiency,
complementation group 2
cell division cycle 27 homolog (S. cerevisiae)
BRCA1 associated RING domain 1
reprimo, TP53 dependent G2 arrest mediator candidate
cullin 4A
similar to 26S protease regulatory subunit 6B (MIP224) (MB67-interacting
protein) (TAT-binding protein 7) (TBP-7); proteasome (prosome,
macropain) 26S subunit, ATPase, 4
SKI-like oncogene
retinoblastoma binding protein 8
discs, large homolog 1 (Drosophila)
TTK protein kinase
NM_004661
NM_001085471
CDC23
foxn3
NM_014885
anapc10
NM_000051
NM_058197
NM_001130156
NM_004847
NM_006814
NM_000455
NM_058195
ATM
CDKN2A
MLF1
Aif1
PSMF1
STK11
CDKN2A
NM_033247
NM_003903
PML
CDC16
NM_033246
NM_014618
NM_006292
NM_015705
NM_000057
NM_014330
NM_014614
PML
DBC1
Tsg101
SGSM3
Blm
PPP1R15A
Psme4
NM_177983
NM_013366
Ppm1g
ANAPC2
NM_033239
NM_016195
NM_000584
NM_002733
NM_001144932
PML
Kif20b
IL8
Prkag1
PSMB5
NM_033238
PML
XM_001714288
NM_002947
NM_002946
NM_002945
NM_004064
NM_004060
NM_014762
NM_014454
NM_005257
NM_002808
NM_002809
ATR
Rpa3
RPA2
RPA1
CDKN1B
ccng1
DHCR24
sesn1
GATA6
PSMD2
psmd3
cell division cycle 23 homolog (S. cerevisiae)
forkhead box N3
anaphase promoting complex subunit 10; anaphase promoting complex
subunit 10 pseudogene
similar to Serine-protein kinase ATM (Ataxia telangiectasia mutated) (A-T,
mutated); ataxia telangiectasia mutated
cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)
myeloid leukemia factor 1
allograft inflammatory factor 1
proteasome (prosome, macropain) inhibitor subunit 1 (PI31)
serine/threonine kinase 11
cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)
promyelocytic leukemia; similar to promyelocytic leukemia protein isoform
1
cell division cycle 16 homolog (S. cerevisiae)
promyelocytic leukemia; similar to promyelocytic leukemia protein isoform
1
deleted in bladder cancer 1
tumor susceptibility gene 101
small G protein signaling modulator 3
Bloom syndrome, RecQ helicase-like
protein phosphatase 1, regulatory (inhibitor) subunit 15A
proteasome (prosome, macropain) activator subunit 4
protein phosphatase 1G (formerly 2C), magnesium-dependent, gamma
isoform
anaphase promoting complex subunit 2
promyelocytic leukemia; similar to promyelocytic leukemia protein isoform
1
kinesin family member 20B
interleukin 8
protein kinase, AMP-activated, gamma 1 non-catalytic subunit
proteasome (prosome, macropain) subunit, beta type, 5
promyelocytic leukemia; similar to promyelocytic leukemia protein isoform
1
ataxia telangiectasia and Rad3 related; similar to ataxia telangiectasia and
Rad3 related protein
replication protein A3, 14kDa
replication protein A2, 32kDa
replication protein A1, 70kDa
cyclin-dependent kinase inhibitor 1B (p27, Kip1)
cyclin G1
24-dehydrocholesterol reductase
sestrin 1
GATA binding protein 6
proteasome (prosome, macropain) 26S subunit, non-ATPase, 2
proteasome (prosome, macropain) 26S subunit, non-ATPase, 3
NM_002806
NM_002807
NM_002066
NM_002804
NM_002805
NM_007182
NM_002803
Psmc6
PSMD1
Gml
psmc3
PSMC5
RASSF1
PSMC2
NM_002800
NM_002166
NM_002801
NM_001126241
NM_001126240
NM_001102667
NM_001143830
NM_001433
NM_003292
NM_004526
NM_002048
NM_001014794
NM_030928
psmb9
ID2
PSMB10
TP73
TP73
Psma4
Gas2
ERN1
tpr
mcm2
GAS1
ILK
Cdt1
NM_001005735
NM_018955
NM_181799
NM_002817
NM_003592
NM_002818
NM_003591
NM_001813
NM_003590
NM_002813
NM_004936
NM_005047
NM_018031
NM_002814
NM_002815
NM_002816
NM_007299
NM_002810
NM_002811
NM_007294
NM_002812
NM_176783
NM_001042383
CHEK2
UBB
UBE2C
PSMD13
CUL1
PSME2
cul2
CENPE
cul3
Psmd9
cdkn2b
PSMD5
Wdr6
PSMD10
Psmd11
PSMD12
BRCA1
PSMD4
psmd7
BRCA1
PSMD8
PSME1
CEP63
proteasome (prosome, macropain) 26S subunit, ATPase, 6
proteasome (prosome, macropain) 26S subunit, non-ATPase, 1
glycosylphosphatidylinositol anchored molecule like protein
proteasome (prosome, macropain) 26S subunit, ATPase, 3
proteasome (prosome, macropain) 26S subunit, ATPase, 5
Ras association (RalGDS/AF-6) domain family member 1
proteasome (prosome, macropain) 26S subunit, ATPase, 2
proteasome (prosome, macropain) subunit, beta type, 9 (large
multifunctional peptidase 2)
inhibitor of DNA binding 2, dominant negative helix-loop-helix protein
proteasome (prosome, macropain) subunit, beta type, 10
tumor protein p73
tumor protein p73
proteasome (prosome, macropain) subunit, alpha type, 4
growth arrest-specific 2
endoplasmic reticulum to nucleus signaling 1
translocated promoter region (to activated MET oncogene)
minichromosome maintenance complex component 2
growth arrest-specific 1
integrin-linked kinase
chromatin licensing and DNA replication factor 1
protein kinase CHK2-like; CHK2 checkpoint homolog (S. pombe); similar to
hCG1983233
ubiquitin B
ubiquitin-conjugating enzyme E2C
proteasome (prosome, macropain) 26S subunit, non-ATPase, 13
cullin 1
proteasome (prosome, macropain) activator subunit 2 (PA28 beta)
cullin 2
centromere protein E, 312kDa
cullin 3
proteasome (prosome, macropain) 26S subunit, non-ATPase, 9
cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)
proteasome (prosome, macropain) 26S subunit, non-ATPase, 5
WD repeat domain 6
proteasome (prosome, macropain) 26S subunit, non-ATPase, 10
proteasome (prosome, macropain) 26S subunit, non-ATPase, 11
proteasome (prosome, macropain) 26S subunit, non-ATPase, 12
breast cancer 1, early onset
proteasome (prosome, macropain) 26S subunit, non-ATPase, 4
proteasome (prosome, macropain) 26S subunit, non-ATPase, 7
breast cancer 1, early onset
proteasome (prosome, macropain) 26S subunit, non-ATPase, 8
proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)
centrosomal protein 63kDa
NM_001042384
NM_001127660
NM_014641
CEP63
MFN2
MDC1
XM_001716106
NM_002969
NM_000296
NM_032955
NM_001013836
NM_152132
NM_001170931
NM_032951
NM_032043
NM_024068
NM_004083
NM_001146274
NM_001042559
NM_005030
NM_001033930
NM_017495
NM_017589
PML
MAPK12
Pkd1
Aif1
MAD1L1
Psma3
FOXO4
Mlxipl
Brip1
OBFC2B
DDIT3
Tcf7l2
EIF4G2
PLK1
uba52
rbm38
BTG4
NM_001184
ATR
NM_002187
NM_005614
NM_005805
NM_001166050
NM_020232
NM_017858
NM_000297
NM_031966
NM_002177
IL12B
rheb
PSMD14
Apbb2
Psmg2
TIPIN
Pkd2
CCNB1
IFNW1
centrosomal protein 63kDa
mitofusin 2
mediator of DNA-damage checkpoint 1
promyelocytic leukemia; similar to promyelocytic leukemia protein isoform
1
mitogen-activated protein kinase 12
polycystic kidney disease 1 (autosomal dominant)
allograft inflammatory factor 1
MAD1 mitotic arrest deficient-like 1 (yeast)
proteasome (prosome, macropain) subunit, alpha type, 3
forkhead box O4
MLX interacting protein-like
BRCA1 interacting protein C-terminal helicase 1
oligonucleotide/oligosaccharide-binding fold containing 2B
DNA-damage-inducible transcript 3
transcription factor 7-like 2 (T-cell specific, HMG-box)
eukaryotic translation initiation factor 4 gamma, 2
polo-like kinase 1 (Drosophila)
ubiquitin A-52 residue ribosomal protein fusion product 1
RNA binding motif protein 38
B-cell translocation gene 4
ataxia telangiectasia and Rad3 related; similar to ataxia telangiectasia and
Rad3 related protein
interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic
lymphocyte maturation factor 2, p40)
Ras homolog enriched in brain
proteasome (prosome, macropain) 26S subunit, non-ATPase, 14
amyloid beta (A4) precursor protein-binding, family B, member 2
proteasome (prosome, macropain) assembly chaperone 2
TIMELESS interacting protein
polycystic kidney disease 2 (autosomal dominant)
cyclin B1
interferon, omega 1
Suppl. Table 2. Table 1 with literature references.
Symbol
Gene
Pattern
Score
Chromo- Regress
some
ion
p-value
Permut Citations and
ation p- PubMed ID
value
Known roles in
cancer
HOXA9
FOXD1
NM_152739
NM_004472
-311.099
-284.649
Chr7
Chr5
7.76E-29
8.72E-21
0.018
0.016
21430775(1)
17943136(2)
CEBPB
BPTF
PAX3
NM_005194
NM_004459
NM_181460
-258.774
-237.042
-257.927
Chr20
Chr17
Chr2
3.68E-12
6.31E-21
5.4E-09
0.015
0.03
0.039
19717648(3)
None
17474900;151
84910(4,5)
myeloma
associated with
placental growth
factor (PLGF)
myeloma
IRF1
TAL1
MZF1
MYC
NM_002198
NM_003189
NM_003422
NM_002467
-231.977
-228.728
-226.479
-206.946
Chr5
Chr1
Chr19
Chr8
7.76E-11
3.4E-10
2.44E-15
3.71E-08
0.012
0.051
0.052
0.06
9022078(6)
15193261(7)
23320102(8)
21468039(9)
NFE2L1
ATF2
NM_003204
NM_001880
-185.26
-160.792
Chr17
Chr2
4.67E-07
2.71E-07
0.018
0.028
None
20029425(10)
STAT3
NM_003150
-159.65
Chr17
6.99E-06
0.057
ATF6
REL
NM_007348
NM_002908
-140.805
-94.9492
Chr1
Chr2
8.68E-06
4.78E-09
0.018
0.047
9022078;1507
0700(6,11)
12902539(12)
11872748(13)
PAX3-FKHR fusion;
chromosomal
rearrangements
myeloma
TAL1/SCL; leukemia
Myeloid malignancies
myeloma;
hyperdiploid
associated with AP-1
complex
myeloma
myeloma
myeloma
References
1
2
3
4
5
6
Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC et al. Initial genome
sequencing and analysis of multiple myeloma. Nature 2011; 471(7339): 467-72.
Myatt SS, Lam EW. The emerging roles of forkhead box (Fox) proteins in cancer. Nature reviews.
Cancer 2007; 7(11): 847-59.
Pal R, Janz M, Galson DL, Gries M, Li S, Johrens K et al. C/EBPbeta regulates transcription factors critical
for proliferation and survival of multiple myeloma cells. Blood 2009; 114(18): 3890-8.
Akalin I, Kutlay NY, Ilhan O, Tukun A. Novel chromosomal translocations in multiple myeloma:
t(13;16)(q14;q24) and t(1;15)(q10;q26). International journal of laboratory hematology 2007; 29(3):
215-20.
Tomescu O, Xia SJ, Strezlecki D, Bennicelli JL, Ginsberg J, Pawel B et al. Inducible short-term and stable
long-term cell culture systems reveal that the PAX3-FKHR fusion oncoprotein regulates CXCR4, PAX3,
and PAX7 expression. Laboratory investigation; a journal of technical methods and pathology 2004;
84(8): 1060-70.
Jelinek DF, Aagaard-Tillery KM, Arendt BK, Arora T, Tschumper RC, Westendorf JJ. Differential human
multiple myeloma cell line responsiveness to interferon-alpha. Analysis of transcription factor
activation and interleukin 6 receptor expression. The Journal of clinical investigation 1997; 99(3): 44756.
7
8
9
10
11
12
13
O'Neil J, Shank J, Cusson N, Murre C, Kelliher M. TAL1/SCL induces leukemia by inhibiting the
transcriptional activity of E47/HEB. Cancer cell 2004; 5(6): 587-96.
Silva G, Cardoso BA, Belo H, Almeida AM. Vorinostat induces apoptosis and differentiation in myeloid
malignancies: genetic and molecular mechanisms. PloS one 2013; 8(1): e53766.
Chng WJ, Huang GF, Chung TH, Ng SB, Gonzalez-Paz N, Troska-Price T et al. Clinical and biological
implications of MYC activation: a common difference between MGUS and newly diagnosed multiple
myeloma. Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K
2011; 25(6): 1026-35.
Lopez-Bergami P, Lau E, Ronai Z. Emerging roles of ATF2 and the dynamic AP1 network in cancer.
Nature reviews. Cancer 2010; 10(1): 65-76.
Bharti AC, Shishodia S, Reuben JM, Weber D, Alexanian R, Raj-Vadhan S et al. Nuclear factor-kappaB
and STAT3 are constitutively active in CD138+ cells derived from multiple myeloma patients, and
suppression of these transcription factors leads to apoptosis. Blood 2004; 103(8): 3175-84.
Lee AH, Iwakoshi NN, Anderson KC, Glimcher LH. Proteasome inhibitors disrupt the unfolded protein
response in myeloma cells. Proceedings of the National Academy of Sciences 2003; 100(17): 9946-51.
Hideshima T, Chauhan D, Richardson P, Mitsiades C, Mitsiades N, Hayashi T et al. NF-kappa B as a
therapeutic target in multiple myeloma. The Journal of biological chemistry 2002; 277(19): 16639-47.
Suppl. Table 3. Table 2 with literature references.
Pattern
Score
Chro
mos
ome
407.6158
383.5932
366.565
352.315
Chr7
Chr8
Chr19
Chr17
RFX1
FOXL1
NM_003109
NM_004430
NM_205843
NM_0010052
91
NM_0011227
41
NM_002918
NM_005250
FOXC1
YY1
E2F1
TFAP2C
Symbol
Gene
SP1
EGR3
NFIC
SREBF1
ESR1
Regressi
on
p-value
Permut
ation pvalue
Citations and
PubMed ID
Known roles in
cancer
1.23E-40
1.67E-21
3.88E-15
1.26E-20
0.011
0.006
0.013
0.032
21856768(1) myeloma
15171706(2) breast cancer
None
12531699(3) breast cancer
312.6539 Chr6
4.75E-25
0.036
10728710(4) myeloma
309.4206 Chr19
292.2963 Chr16
8.29E-23
7.02E-10
0.028
0.026
NM_001453
289.9529 Chr6
1.54E-16
0.055
NM_003403
NM_005225
NM_003222
254.8226 Chr14
252.5363 Chr20
245.9572 Chr20
1.11E-06
9.85E-15
1E-23
0.029
0.025
0.036
None
17089004;179431 colon cancer;
36(5,6) gastrointestinal
21465172(7) associated with
VEGF expression;
cancer
16314846(8) cancer biology
21889194(9) myeloma; Myc
18825690(10) invasive breast
cancer
References
1
2
3
4
5
6
7
8
9
Fulciniti M, Amin S, Nanjappa P, Rodig S, Prabhala R, Li C et al. Significant biological role of sp1
transactivation in multiple myeloma. Clinical cancer research : an official journal of the American
Association for Cancer Research 2011; 17(20): 6500-9.
Inoue A, Omoto Y, Yamaguchi Y, Kiyama R, Hayashi SI. Transcription factor EGR3 is involved in the
estrogen-signaling pathway in breast cancer cells. Journal of molecular endocrinology 2004; 32(3): 64961.
Yang Y, Morin PJ, Han WF, Chen T, Bornman DM, Gabrielson EW et al. Regulation of fatty acid synthase
expression in breast cancer by sterol regulatory element binding protein-1c. Experimental cell research
2003; 282(2): 132-7.
Otsuki T, Yamada O, Kurebayashi J, Moriya T, Sakaguchi H, Kunisue H et al. Estrogen receptors in
human myeloma cells. Cancer research 2000; 60(5): 1434-41.
Katoh Y, Katoh M. Hedgehog signaling pathway and gastrointestinal stem cell signaling network
(review). International journal of molecular medicine 2006; 18(6): 1019-23.
Myatt SS, Lam EW. The emerging roles of forkhead box (Fox) proteins in cancer. Nature reviews.
Cancer 2007; 7(11): 847-59.
Du J, Li L, Ou Z, Kong C, Zhang Y, Dong Z et al. FOXC1, a target of polycomb, inhibits metastasis of
breast cancer cells. Breast cancer research and treatment 2012; 131(1): 65-73.
Gordon S, Akopyan G, Garban H, Bonavida B. Transcription factor YY1: structure, function, and
therapeutic implications in cancer biology. Oncogene 2006; 25(8): 1125-42.
Delmore JE, Issa GC, Lemieux ME, Rahl PB, Shi J, Jacobs HM et al. BET bromodomain inhibition as a
therapeutic strategy to target c-Myc. Cell 2011; 146(6): 904-17.
10
Gee JM, Eloranta JJ, Ibbitt JC, Robertson JF, Ellis IO, Williams T et al. Overexpression of TFAP2C in
invasive breast cancer correlates with a poorer response to anti-hormone therapy and reduced patient
survival. The Journal of pathology 2009; 217(1): 32-41.
Suppl. Table 4. TrF enrichment p-value and differential expression p-value.
TrF
MYC
CREB1
E2F3
MYB
USF2
HSF2
E2F5
NFYB
ATF2
E2F2
POU6F1
NFYC
HSF1
PAX3
MAX
E2F1
MYCN
ELK1
YY1
ETS1
E2F4
PLAU
TAL1
HIVEP2
PBX1
Enrichment p-value of
TrF targets in cell cycle
arrest genes (p<0.05)
0.040472013
0.007794102
0.002375234
0.006847614
0.042884464
0.031170154
0.002375234
0.001542229
0.000416396
0.002375234
0.020160309
0.000874621
0.013469371
0.022682979
0.006349611
0.01650009
0.02610581
0.029106112
0.02519478
0.037115929
0.002375234
0.040820826
0.038511889
0.021316004
0.019285905
HMM-NHMM
differential
expression p-value
0.00018
0.004
0.007
0.032
0.034
0.074
0.15
0.16
0.2
0.21
0.29
0.31
0.32
0.42
0.44
0.44
0.49
0.56
0.58
0.61
0.63
0.65
0.69
0.89
0.9
HMM-NHMM t statistics
(positive values for higher
expression in HMM)
3.85
-2.07
2.73
-2.17
2.15
1.8
1.44
1.4
-1.29
1.25
-1.05
-1.02
0.997
0.81
-0.77
-0.77
0.69
-0.59
-0.56
0.52
-0.48
0.46
-0.4
0.14
-0.13