Supplementary Figure and Table - media.nature.com · Supplementary Figure 2. In situ detection of...

Supplementary Figure 1. The tumors formed in NOD/SCID mice by α2δ1+ and α2δ1– subpopulations isolated from HCC cell lines and primary HCC samples. 1°, primary transplantation; 2°, second transplantation.

Supplementary Figure 2. In situ detection of let-7c, miR-200b, miR-222 and miR-424 (green), together with DAPI staining (blue) for nuclear in both Hep-11 and Hep-12 cell lines (A), as well as in FACS purified α2δ1－ and α2δ1+ Huh7 cells (B). Parallel α2δ1 staining is shown to demonstrate the α2δ1 staining pattern of respective cells. Bar=50 μm.

Supplementary Figure 3. qRT-PCR analysis of indicated miRNA levels in Hep-12 cells (A-D) overexpressing indicated miRNAs, and in Huh7 cells (E-H) with indicated miRNAs knocked-down by Tud RNAs against indicated miRNAs .

Supplementary Figure 4. Uncropped western blots. a, For Fig. 3i; b, For Fig. 3j; c, For Fig. 4c; d, For Fig. 4e.

Supplementary Figure 5. Uncropped western blots. a, For Fig. 5b; b, For Fig. 5d; c, For Fig. 5f; d, For Fig. 5h.

Supplementary Figure 6. Uncropped western blots. a, For Fig. 6f; b, For Fig. 6g; c, For Fig. 6n

Supplementary Figure 7. Uncropped western blots. a, For Fig.7a; b, For Fig. 7c; c, For Fig. 7e; d, For Fig. 7g; e, For Fig. 7h; f, For Fig. 7i.

Supplementary Table 1. Relationships between the expression of α2δ1 mRNA

and the clinicopathologic features in 85 HCC patients

Variable Cases

(n)

α2δ1 expression

(RQ: 2－ Ct) P-value a

Median Range

Gender Male 74 1.26 0.003-46.45- 0.465

Female 11 1.39 0.29-161.99

Age (year) ≤60 63 1.30 0.003-46.45 0.256

>60 22 1.12 0.21-161.99

Cirrhosis Absent 27 0.84 0.003-15.69 0.728

Present 58 1.53 0.21-161.99

Size (cm) ≤5 45 0.82 0.003-39.31 0.030

>5 40 1.94 0.25-161.99

Venous invasion Absent 63 1.27 0.003-161.99 0.173

Present 22 1.56 0.26-46.45

Survival (year) <4 40 1.777 0.003-161.99 0.046

≥4 45 1.187 0.21-8.693

Recurrence Yes b 41 1.87 0.003-161.99 0.0096

No c 44 0.99 0.09-15.69 aMann–Whitney test. bRecurrences occur within 2 years of diagnosis. cNo recurrences found within 4 years of diagnosis.

Supplementary Table 2. Cox regression analysis of clinicopathological features and α2δ1 expression in 85 HCC patients

Variable Cases

(n)

Multivariate analysisa

RR(95%CI) P-value

Sex Male 74 1.379 0.653

Female 11 0.565-3.363

Age (year) ≤60 63 1.380 0.281

>60 22 0.641–2.972

Cirrhosis Absent 27 0.502 0.023

Present 58 0.231–1.091

Size (cm) ≤5 45 7.044 0.009

>5 40 2.660-18.665

Venous invasion Present 22 1.562 0.024

Absent 63 1.155-2.113

α2δ1 expressionb High 43 2.662 0.005

Low 42 1.355-5.232

a COX regression analysis.

bThe patients are classified according to the median level of α2δ1 expression.

Abbreviations: RR, Relative risk; CI, Confidence interval.

Supplementary Table 3. The relationships between the expression of PBX3 mRNA

and the clinicopathologic features in 85 HCC patients

Variable Cases

(n)

PBX3 expression (RQ: 2－ Ct) P-value a

Median Range

Gender Male 74 2.51 0.01-62850 0.260

Female 11 3.72 0.10-46.51

Age (year) ≤60 63 3.16 0.01-371.6 0.474

>60 22 3.01 0.06-62850

Cirrhosis Absent 27 1.51 0.01-56.43 0.028

Present 58 3.83 0.06-62850

Size (cm) ≤5 45 1.51 0.01-5535 0.038

>5 40 4.48 0.06-62850

Venous invasion Absent 63 2.67 0.01-62850 0.313

Present 22 2.30 0.06-371.6

Survival (year) <4 40 3.94 0.01-62850 0.024

≥4 45 2.16 0.06-138.3

Recurrence Yes b 41 3.38 0.09-62850 0.0074

No c 44 1.56 0.01-53.26 aMann–Whitney test. bRecurrences occur within 2 years of diagnosis. cNo recurrences detected within 4 years of diagnosis.

Supplementary Table 4. Cox regression analysis of clinicopathological features and

PBX3 expression in 85 HCC patients

Variable Cases(n)

Multivariate analysisa

RR(95%CI) P-value

Sex Male 74 0.824 0.668

Female 11 0.339 - 2.000

Age (year) ≤60 63 1.493 0.368

>60 22 0.633 - 3.519

Cirrhosis Absent 27 0.463 0.102

Present 58 0.184 - 1.116

Size (cm) ≤5 45 2.406 0.035

>5 40 1.065 - 5.434

Venous invasion Absent 63 0.318 0.005

Present 22 0.143 - 0.707

PBX3b High 44 2.935 0.008

Low 41 1.329 - 6.483

a COX regression analysis.

bThe patients are classified according to the median level of PBX3 mRNA.

Abbreviation: RR: Relative risk, CI: Confidence interval

Supplementary Table 5. PBX3 responsive genes as revealed by RNA‐seq analysis of SMMC‐7721 cells

upon forced expression of PBX3 compared with vector control

Up‐regulated genes after PBX3 over‐expression

Gene Symbol Gene name Ratio

BG alpha‐1‐B glycoprotein 41.51

ABCB1 ATP‐binding cassette, sub‐family B (MDR/TAP), member 1 3.89

ABHD1 abhydrolase domain containing 1 2.83

ABI1 abl‐interactor 1 2.64

ABI3 ABI family, member 3 17.82

ACOT6 acyl‐CoA thioesterase 6 2.64

ACSL6 acyl‐CoA synthetase long‐chain family member 6 8.24

ACSM2A acyl‐CoA synthetase medium‐chain family member 2A 67.83

ADAM28 ADAM metallopeptidase domain 28 95.57

ADCY2 adenylate cyclase 2 (brain) 30.73

ADPGK ADP‐dependent glucokinase 31.65

AHSP erythroid associated factor 476.19

AKR1B15 aldo‐keto reductase family 1, member B10 (aldose reductase) 32.25

ALDOC aldolase C, fructose‐bisphosphate 3.11

ALOX12B arachidonate 12‐lipoxygenase, 12R type 2.59

ALOX5 arachidonate 5‐lipoxygenase 16.66

ALOXE3 arachidonate lipoxygenase 3 28.09

AMBP alpha‐1‐microglobulin/bikunin precursor 2.19

AMN amnionless homolog (mouse) 32.11

ANGPTL3 angiopoietin‐like 3 254.27

ANK1 ankyrin 1, erythrocytic 10.05

ANK2 ankyrin 2, neuronal 16.88

ANKRD12 ankyrin repeat domain 12 2.45



ANO2 anoctamin 2 10.38

APCDD1L adenomatosis polyposis coli down‐regulated 1‐like 29.48

APLN apelin 2.47

APOA1 apolipoprotein A‐I 41.18

APOBEC2 apolipoprotein B mRNA editing enzyme, catalytic polypeptide‐like 2 40.57

ARHGAP15 Rho GTPase activating protein 15 19.52



ARL17B ADP‐ribosylation factor‐like 17 pseudogene 1 2.09

ARR3 arrestin 3, retinal (X‐arrestin) 107.00

ARSD arylsulfatase D 27.50

ART1 ADP‐ribosyltransferase 1 150.86

ASGR1 asialoglycoprotein receptor 1 37.87

ASPN asporin 79.26

ATF3 activating transcription factor 3 3.05

ATG9B ATG9 autophagy related 9 homolog B (S. cerevisiae) 2.67

ATP6V0A4 ATPase, H+ transporting, lysosomal V0 subunit a4 29.29

ATXN3 ataxin 3 2.16

B3GNT8 UDP‐GlcNAc:betaGal beta‐1,3‐N‐acetylglucosaminyltransferase 8 4.04

BCL2L14 BCL2‐like 14 (apoptosis facilitator) 98.77

BCL2L2 BCL2‐like 2 2.14

BEST2 bestrophin 2 148.04

BEST4 bestrophin 4 2.90

BMP5 bone morphogenetic protein 5 10.17

BNIP3 BCL2/adenovirus E1B 19kDa interacting protein 3 3.65

BOC Boc homolog (mouse) 17.75

C10orf10 chromosome 10 open reading frame 10 2.41



C16orf11 hypothetical protein FLJ36208; chromosome 16 open reading frame

11

89.71




C2 complement component 2 3.21






C7 complement component 7 12.95





CA9 carbonic anhydrase IX 5.56

CABP7 calcium binding protein 7 2.36

CACNA2D1 calcium channel, voltage‐dependent, alpha 2/delta subunit 1 2884.80

CAMK4 calcium/calmodulin‐dependent protein kinase IV 11.77

CAPN5 calpain 5 4.75

CARD18 caspase recruitment domain family, member 18 14.45

CASC1 cancer susceptibility candidate 1 26.48

CASQ1 calsequestrin 1 (fast‐twitch, skeletal muscle) 2.16

CCDC105 coiled‐coil domain containing 105 115.02








CD70 CD70 molecule 2.12

CD79A CD79a molecule, immunoglobulin‐associated alpha 16.39

CDK18 PCTAIRE protein kinase 3 2.52

CEACAM16 carcinoembryonic antigen‐related cell adhesion molecule 16 188.20

CEACAM19 carcinoembryonic antigen‐related cell adhesion molecule 19 15.11

CES3 carboxylesterase 3 9.76

CHD5 chromodomain helicase DNA binding protein 5 2.26

CHRNB4 cholinergic receptor, nicotinic, beta 4 24.77

CHRNG cholinergic receptor, nicotinic, gamma 32.30

CIB2 calcium and integrin binding family member 2 27.21

CISH cytokine inducible SH2‐containing protein 19.48

CLCA2 chloride channel accessory 2 7.00

CLDN7 claudin 7 3.75

CLEC14A C‐type lectin domain family 14, member A 16.89

CLGN calmegin 2.11

CLIC3 chloride intracellular channel 3 2.52

CLIP3 CAP‐GLY domain containing linker protein 3 2.81

CLUL1 clusterin‐like 1 (retinal) 13.16

CNIH3 cornichon homolog 3 (Drosophila) 19.49

CNTNAP2 contactin associated protein‐like 2 3.05

COL13A1 collagen, type XIII, alpha 1 35.02

COL4A3 collagen, type IV, alpha 3 (Goodpasture antigen) 4.81

CPLX3 complexin 3 71.78

CPNE5 copine V 73.87

CPXM2 carboxypeptidase X (M14 family), member 2 3.41

CRYGS crystallin, gamma S 47.87

CSTA cystatin A (stefin A) 5.54

CTSW cathepsin W 26.06

CXCR5 chemokine (C‐X‐C motif) receptor 5 15.22

CYP39A1 cytochrome P450, family 39, subfamily A, polypeptide 1 2.86

CYP4X1 cytochrome P450, family 4, subfamily X, polypeptide 1 59.79

CYP8B1 cytochrome P450, family 8, subfamily B, polypeptide 1 50.99

DBNDD1 dysbindin (dystrobrevin binding protein 1) domain containing 1 17.44

DGKI diacylglycerol kinase, iota 9.37

DHDH dihydrodiol dehydrogenase (dimeric) 22.65

DHH desert hedgehog homolog (Drosophila) 27.78

DHRS9 dehydrogenase/reductase (SDR family) member 9 7.25

DIRAS1 DIRAS family, GTP‐binding RAS‐like 1 7.16

DNAJB5 DnaJ (Hsp40) homolog, subfamily B, member 5 2.25

DNAJC28 DnaJ (Hsp40) homolog, subfamily C, member 28 2.23

DNALI1 dynein, axonemal, light intermediate chain 1 22.53

DPCR1 diffuse panbronchiolitis critical region 1 15.96

DPPA4 developmental pluripotency associated 4 11.40

DSE dermatan sulfate epimerase 2.70

DUOX2 dual oxidase 2 2.16

EFEMP2 EGF‐containing fibulin‐like extracellular matrix protein 2 5.30

EFHD1 EF‐hand domain family, member D1 18.39

EGFL8 EGF‐like‐domain, multiple 8 2.44

EIF4ENIF1 eukaryotic translation initiation factor 4E nuclear import factor 1 2.10

ELAVL3 ELAV (embryonic lethal, abnormal vision, Drosophila)‐like 3 (Hu

antigen C)

30.49

ELOVL7 ELOVL family member 7, elongation of long chain fatty acids (yeast) 2.24

ELTD1 EGF, latrophilin and seven transmembrane domain containing 1 17.58

EMILIN3 elastin microfibril interfacer 3 2.95

EMR1 egf‐like module containing, mucin‐like, hormone receptor‐like 1 12.87

ENKUR enkurin, TRPC channel interacting protein 34.55

ENPP7 ectonucleotide pyrophosphatase/phosphodiesterase 7 32.87

EPCAM epithelial cell adhesion molecule 24.20

EPN2 epsin 2 2.88

ESF1 similar to ABT1‐associated protein; ESF1, nucleolar pre‐rRNA

processing protein, homolog (S. cerevisiae)

11.30

EXTL1 exostoses (multiple)‐like 1 15.88

EYA2 eyes absent homolog 2 (Drosophila) 77.76

FAM109B family with sequence similarity 109, member B 13.31

FAM117A family with sequence similarity 117, member A 3.84


FAM196A chromosome 10 open reading frame 141 45.70

FAM19A3 family with sequence similarity 19 (chemokine (C‐C motif)‐like),

member A3

24.31

FAM25C family with sequence similarity 25, member C 300.60


FBLN2 fibulin 2 19.19

FBXO24 F‐box protein 24 17.78

FCGR1A Fc fragment of IgG, high affinity Ic, receptor (CD64) 13.19

FCRL6 Fc receptor‐like 6 18.65

FCRLB Fc receptor‐like B 5.29

FER1L5 fer‐1‐like 5 (C. elegans) 25.03


FFAR1 free fatty acid receptor 1 19.14

FGD2 FYVE, RhoGEF and PH domain containing 2 22.35


FGF22 fibroblast growth factor 22 2.64

FGGY FGGY carbohydrate kinase domain containing 32.46

FKBP1B FK506 binding protein 1B, 12.6 kDa 18.24

FLG2 filaggrin family member 2 10.52

FLJ22184 hypothetical protein FLJ22184 2.25

FLJ44635 TPT1‐like protein 17.26

FMN1 formin 1 15.46

FOXD4L1 forkhead box D4‐like 1 40.44

FOXS1 forkhead box S1 148.86

FRK fyn‐related kinase 2.10

FRMPD4 FERM and PDZ domain containing 4 6.22

FSIP2 fibrous sheath interacting protein 2 13.29

FSTL4 follistatin‐like 4 8.83

FUZ fuzzy homolog (Drosophila) 2.41

GAB2 GRB2‐associated binding protein 2 2.75

GABBR2 gamma‐aminobutyric acid (GABA) B receptor, 2 8.50

GAL3ST1 galactose‐3‐O‐sulfotransferase 1 128.88

GALNT12 UDP‐N‐acetyl‐alpha‐D‐galactosamine:polypeptide

N‐acetylgalactosaminyltransferase 12 (GalNAc‐T12)

4.15


N‐acetylgalactosaminyltransferase 8 (GalNAc‐T8)

94.33

GEM GTP binding protein overexpressed in skeletal muscle 112.38

GIMAP1 GTPase, IMAP family member 1 11.28

GIMAP8 GTPase, IMAP family member 8 22.65

GLIS1 GLIS family zinc finger 1 21.91

GNGT1 guanine nucleotide binding protein (G protein), gamma transducing

activity polypeptide 1

49.22

GNRHR gonadotropin‐releasing hormone receptor 9.92

GOLGA6D golgi autoantigen, golgin subfamily a, 6D 12.41

GOLGA6L6 Putative golgin subfamily A member 6‐like protein 6 10.76

GPA33 glycoprotein A33 (transmembrane) 22.00

GPIHBP1 glycosylphosphatidylinositol anchored high density lipoprotein

binding protein 1

19.81

GPNMB glycoprotein (transmembrane) nmb 2.25

GPR155 G protein‐coupled receptor 155 33.09




GRAMD3 GRAM domain containing 3 2.13

GRIK2 glutamate receptor, ionotropic, kainate 2 4.20

GRIP2 glutamate receptor interacting protein 2 2.75

GSTA2 glutathione S‐transferase alpha 2 152.58

GULP1 GULP, engulfment adaptor PTB domain containing 1 2.90

HAAO 3‐hydroxyanthranilate 3,4‐dioxygenase 154.80

HAPLN2 hyaluronan and proteoglycan link protein 2 2.64

HIC1 hypermethylated in cancer 1 24.58

HIF1A hypoxia inducible factor 1, alpha subunit (basic helix‐loop‐helix

transcription factor)

16.95

HIST1H3J histone cluster 1, H3j 2.00

HIST1H4A histone cluster 1, H4a 19.39

HLA‐DRB4 major histocompatibility complex, class II, DR beta 4 16.83

HOXC12 homeobox C12 290.54

HOXD3 homeobox D3 2.29

HS3ST3B1 heparan sulfate (glucosamine) 3‐O‐sulfotransferase 3B1 2.05

HSPB2 heat shock 27kDa protein 2 28.07

HSPB7 heat shock 27kDa protein family, member 7 (cardiovascular) 64.69

IFNA8 interferon, alpha 8 18.04

IGFBP2 insulin‐like growth factor binding protein 2, 36kDa 197.93

IGFBP5 insulin‐like growth factor binding protein 5 14.42

IL17D interleukin 17D 3.58

IL1RAP interleukin 1 receptor accessory protein 33.89

INHBC inhibin, beta C 2.02

INMT indolethylamine N‐methyltransferase 13.90

INSM2 insulinoma‐associated 2 3.05

IQUB IQ motif and ubiquitin domain containing 46.59

ISPD notch1‐induced protein 3.24

ITGAL integrin, alpha L (antigen CD11A (p180), lymphocyte

function‐associated antigen 1; alpha polypeptide)

13.93

ITGBL1 integrin, beta‐like 1 (with EGF‐like repeat domains) 21.97

JAZF1 JAZF zinc finger 1 32.89

JSRP1 junctional sarcoplasmic reticulum protein 1 6.48

KAT6B K(lysine) acetyltransferase 6B 2.23

KATNAL1 katanin p60 subunit A‐like 1 2.63

KCNB1 potassium voltage‐gated channel, Shab‐related subfamily, member 1 131.34

KCNC1 potassium voltage‐gated channel, Shaw‐related subfamily, member 1 43.60

KCND2 potassium voltage‐gated channel, Shal‐related subfamily, member 2 15.92

KCNE3 potassium voltage‐gated channel, Isk‐related family, member 3 14.84

KCNJ14 potassium inwardly‐rectifying channel, subfamily J, member 14 2.12

KCNK2 potassium channel, subfamily K, member 2 19.87

KCNQ5 potassium voltage‐gated channel, KQT‐like subfamily, member 5 11.18

KCNS1 potassium voltage‐gated channel, delayed‐rectifier, subfamily S,

member 1

32.23

KCTD12 potassium channel tetramerisation domain containing 12 2.29

KIAA1045 KIAA1045 15.08

KIAA1324 KIAA1324 7.80

KIAA1462 KIAA1462 9.85

KIAA1683 KIAA1683 2.34

KIF26B kinesin family member 26B 19.26

KIRREL3 kin of IRRE like 3 (Drosophila) 3.24

KLHL32 kelch‐like 32 (Drosophila) 6.06


KLRF1 killer cell lectin‐like receptor subfamily F, member 1 40.41

KRT20 keratin 20 2.41



LAIR1 leukocyte‐associated immunoglobulin‐like receptor 1 11.71

LEPR leptin receptor 15.92

LGALS4 lectin, galactoside‐binding, soluble, 4 540.41

LHB luteinizing hormone beta polypeptide 25.42

LHCGR luteinizing hormone/choriogonadotropin receptor 14.78

LIMS2 LIM and senescent cell antigen‐like domains 2 47.15

LIN28A lin‐28 homolog (C. elegans) 10.45

LIPC lipase, hepatic 28.94

LIPN lipase, family member N 2.86

LOC100129924 similar to hCG2036949 2.44

LOC100287036 hypothetical protein LOC100287036 6.17

LOC388813 uncharacterized protein ENSP00000383407‐like 226.55

LOC554223 hypothetical LOC554223 86.05

LOC728392 hypothetical protein LOC728392 2.75

LOXL4 lysyl oxidase‐like 4 7.86

LRRC17 leucine rich repeat containing 17 14.84




LY6D lymphocyte antigen 6 complex, locus D 28.96

MAF v‐maf musculoaponeurotic fibrosarcoma oncogene homolog (avian) 47.09

MAGI2 membrane associated guanylate kinase, WW and PDZ domain

containing 2

4.51

MANSC1 MANSC domain containing 1 2.83

MAP7D2 MAP7 domain containing 2 10.41

MARCO macrophage receptor with collagenous structure 99.25

MAT1A methionine adenosyltransferase I, alpha 28.12

MB myoglobin 3.06

MED12L mediator complex subunit 12‐like 4.51

MFSD2B hypothetical protein LOC388931 163.57

MLIP muscular LMNA‐interacting protein 30.43

MMP23B matrix metallopeptidase 23A (pseudogene); matrix metallopeptidase

23B

2.31

MRAP2 melanocortin 2 receptor accessory protein 2 7.37

MSI1 musashi homolog 1 (Drosophila) 67.82

MTL5 metallothionein‐like 5, testis‐specific (tesmin) 3.79

MXD1 MAX dimerization protein 1 11.17

MYBPC2 myosin binding protein C, fast type 39.58

MYBPC3 myosin binding protein C, cardiac 3.24

MYLK3 myosin light chain kinase 3 2.67

MYO1A myosin IA 13.60

MYOZ1 myozenin 1 53.69

NEGR1 neuronal growth regulator 1 3.43

NEU2 sialidase 2 (cytosolic sialidase) 768.05

NGFR nerve growth factor receptor (TNFR superfamily, member 16) 29.83

NHLRC4 hypothetical protein FLJ36208; chromosome 16 open reading frame

11

3.05

NKD2 naked cuticle homolog 2 (Drosophila) 14.87

NOL3 nucleolar protein 3 (apoptosis repressor with CARD domain) 2.21

NOS3 nitric oxide synthase 3 (endothelial cell) 4.36

NOSTRIN nitric oxide synthase trafficker 25.09

NOTCH3 Notch homolog 3 (Drosophila) 17.18

NOVA2 neuro‐oncological ventral antigen 2 185.06

NPL N‐acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase) 11.92

NPW neuropeptide W 2.16

NPY5R neuropeptide Y receptor Y5 73.56

NR5A1 nuclear receptor subfamily 5, group A, member 1 14.78


NTF4 neurotrophin 4 450.80

NTNG2 netrin G2 20.84

NXNL2 nucleoredoxin‐like 2 3.83

NYNRIN KIAA1305 38.45

ODAM odontogenic, ameloblast asssociated 55.84

OLFM2 olfactomedin 2 29.83

OMD osteomodulin 112.05

OMG oligodendrocyte myelin glycoprotein 2.07

OR13A1 olfactory receptor, family 13, subfamily A, member 1 12.75

OR4F21 olfactory receptor, family 4, subfamily F, member 21 26.83

OR6K3 olfactory receptor, family 6, subfamily K, member 3 26.71

ORAI3 ORAI calcium release‐activated calcium modulator 3 2.29

OTOGL otogelin‐like 24.92

OVOL1 ovo‐like 1(Drosophila) 2.16

P2RX3 purinergic receptor P2X, ligand‐gated ion channel, 3 60.93

P4HA1 prolyl 4‐hydroxylase, alpha polypeptide I 8.17

PAK4 p21 protein (Cdc42/Rac)‐activated kinase 4 2.31

PALM3 Paralemmin‐3 50.43

PAPPA2 pappalysin 2 46.30

PARK2 Parkinson disease (autosomal recessive, juvenile) 2, parkin 9.27

PBOV1 prostate and breast cancer overexpressed 1 12.94

PBX3 pre‐B‐cell leukemia homeobox 3 88.94

PCDHA9 protocadherin alpha 9 2.16

PCOLCE procollagen C‐endopeptidase enhancer 211.29

PDE6G phosphodiesterase 6G, cGMP‐specific, rod, gamma 21.42

PDGFC platelet derived growth factor C 5.64

PDIA2 protein disulfide isomerase family A, member 2 233.37

PDK3 pyruvate dehydrogenase kinase, isozyme 3 2.65

PDLIM4 PDZ and LIM domain 4 19.77

PIWIL4 piwi‐like 4 (Drosophila) 20.51

PKD1L1 polycystic kidney disease 1 like 1 14.95

PLA2G4D phospholipase A2, group IVD (cytosolic) 130.30

PLAG1 pleiomorphic adenoma gene 1 18.21

PLAT plasminogen activator, tissue 5.04

PLEKHA4 pleckstrin homology domain containing, family A (phosphoinositide

binding specific) member 4

5.49

PLXDC1 plexin domain containing 1 2.58

PLXNA4 plexin A4 39.31

POPDC2 popeye domain containing 2 2.75

PPFIA1 protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF),

interacting protein (liprin), alpha 1

2.03


interacting protein (liprin), alpha 4

4.41

PPP1R1C protein phosphatase 1, regulatory (inhibitor) subunit 1C 223.65


PRELID2 PRELI domain containing 2 3.10

PRKAG2 protein kinase, AMP‐activated, gamma 2 non‐catalytic subunit 2.52

PRKAR2B protein kinase, cAMP‐dependent, regulatory, type II, beta 35.87

PRND prion protein 2 (dublet) 2.52

PRPH peripherin 55.44

PRR23C FLJ46210 protein 23.35

PRSS16 protease, serine, 16 (thymus) 2.11

PTAFR platelet‐activating factor receptor 11.49

PTPRC protein tyrosine phosphatase, receptor type, C 12.89

PTPRE protein tyrosine phosphatase, receptor type, E 2.37

PTPRH protein tyrosine phosphatase, receptor type, H 3.09

PTPRR protein tyrosine phosphatase, receptor type, R 54.15

RAB43 RAB43, member RAS oncogene family; hypothetical LOC100131426 18.55

RAG1 recombination activating gene 1 3.74

RAPGEF5 Rap guanine nucleotide exchange factor (GEF) 5 30.38

RARRES1 retinoic acid receptor responder (tazarotene induced) 1 33.08

RASSF4 Ras association (RalGDS/AF‐6) domain family member 4 4.32

RBPJL recombination signal binding protein for immunoglobulin kappa J

region‐like

27.77

RCN3 reticulocalbin 3, EF‐hand calcium binding domain 3.87

RDX radixin 2.01

RFESD Rieske (Fe‐S) domain containing 2.48

RFX3 regulatory factor X, 3 (influences HLA class II expression) 23.46

RGAG1 retrotransposon gag domain containing 1 3.24

RGMA RGM domain family, member A 18.12

RIN2 Ras and Rab interactor 2 11.91

RNASEK ribonuclease, RNase K 21.06

RNF182 ring finger protein 182 2.13


ROS1 c‐ros oncogene 1 , receptor tyrosine kinase 2.11

RPS6KB1 ribosomal protein S6 kinase, 70kDa, polypeptide 1 2.21

RTDR1 rhabdoid tumor deletion region gene 1 39.71

RTN4RL2 reticulon 4 receptor‐like 2 3.52

SALL2 sal‐like 2 (Drosophila) 6.24

SCARF2 scavenger receptor class F, member 2 12.00

SCG5 secretogranin V (7B2 protein) 36.45

SCGB1D2 secretoglobin, family 1D, member 2 627.37

SCN2B sodium channel, voltage‐gated, type II, beta 8.43

SCT secretin 479.89

SDC2 syndecan 2 6.96

SEMA5A sema domain, seven thrombospondin repeats (type 1 and type

1‐like), transmembrane domain (TM) and short cytoplasmic domain,

(semaphorin) 5A

2.44

SERPINC1 serpin peptidase inhibitor, clade C (antithrombin), member 1 31.09

SERPINE3 serpin peptidase inhibitor, clade E (nexin, plasminogen activator

inhibitor type 1), member 3

21.66

SERPINF2 serpin peptidase inhibitor, clade F (alpha‐2 antiplasmin, pigment

epithelium derived factor), member 2

17.57

SFMBT2 Scm‐like with four mbt domains 2 9.62

SGK2 serum/glucocorticoid regulated kinase 2 20.06

SGOL1 shugoshin‐like 1 (S. pombe) 9.40


SH3YL1 SH3 domain containing, Ysc84‐like 1 (S. cerevisiae) 3.05

SHISA7 UPF0626 protein A 10.58

SIAH3 seven in absentia homolog 3 (Drosophila) 35.56

SIGIRR single immunoglobulin and toll‐interleukin 1 receptor (TIR) domain 14.52

SLC14A2 solute carrier family 14 (urea transporter), member 2 9.59

SLC22A11 solute carrier family 22 (organic anion/urate transporter), member

11

111.92

SLC22A14 solute carrier family 22, member 14 36.99

SLC2A14 solute carrier family 2 (facilitated glucose transporter), member 14 35.10

SLC2A5 solute carrier family 2 (facilitated glucose/fructose transporter),

member 5

2.06

SLC37A2 solute carrier family 37 (glycerol‐3‐phosphate transporter), member

2

13.93


SLC5A2 solute carrier family 5 (sodium/glucose cotransporter), member 2 24.36

SLC6A8 solute carrier family 6 (neurotransmitter transporter, creatine),

member 8

63.59

SLC8A2 solute carrier family 8 (sodium/calcium exchanger), member 2 32.53

SLCO1A2 solute carrier organic anion transporter family, member 1A2 7.14

SLCO1B1 solute carrier organic anion transporter family, member 1B1 101.72

SLCO1B7 solute carrier organic anion transporter family, member 1B7 4.04

SMARCD3 SWI/SNF related, matrix associated, actin dependent regulator of

chromatin, subfamily d, member 3

2.28

SMTN smoothelin 3.53

SNX20 sorting nexin 20 43.10

SOX2 SRY (sex determining region Y)‐box 2 3.74

SPACA4 sperm acrosome associated 4 26.29

SPTY2D1 SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae) 24.41

SRCRB4D scavenger receptor cysteine rich domain containing, group B (4

domains)

2.16

SRMS src‐related kinase lacking C‐terminal regulatory tyrosine and

N‐terminal myristylation sites

4.95

STX1A syntaxin 1A (brain) 19.62

SULT1A2 sulfotransferase family, cytosolic, 1A, phenol‐preferring, member 2 2.22

SWT1 Transcriptional protein SWT1 11.15

SYCP2 synaptonemal complex protein 2 2.00

SYCP2L synaptonemal complex protein 2‐like 6.67

SYN2 synapsin II 2.64

TACR1 tachykinin receptor 1 51.44

TAF7L TAF7‐like RNA polymerase II, TATA box binding protein

(TBP)‐associated factor, 50kDa

16.89

TAS2R5 taste receptor, type 2, member 5 2.25

TBC1D3C TBC1 domain family, member 3C 22.31

TBX19 T‐box 19 2.14

TCEAL3 transcription elongation factor A (SII)‐like 3 3.26

TCTE3 t‐complex‐associated‐testis‐expressed 3 54.93

TEK TEK tyrosine kinase, endothelial 25.59

TFEC transcription factor EC 8.70

THY1 Thy‐1 cell surface antigen 16.15

TICAM2 transmembrane emp24 protein transport domain containing 7;

toll‐like receptor adaptor molecule 2

30.55

TLR9 toll‐like receptor 9 32.16

TM4SF19 transmembrane 4 L six family member 19 2.80

TMEM119 transmembrane protein 119 52.73

TMEM191C transmembrane protein 191B; transmembrane protein 191C 34.32

TMEM63C transmembrane protein 63C 2.34


TNFRSF13B tumor necrosis factor receptor superfamily, member 13B 547.26

TOX thymocyte selection‐associated high mobility group box 168.89

TP53INP2 tumor protein p53 inducible nuclear protein 2 2.13

TP53TG5 TP53 target 5 18.43

TRAF5 TNF receptor‐associated factor 5 3.54

TREM1 triggering receptor expressed on myeloid cells 1 466.94

TRIM39 tripartite motif‐containing 39 16.63



TSHZ2 teashirt zinc finger homeobox 2 7.55

TSPAN5 tetraspanin 5 3.51


UBE2W ubiquitin‐conjugating enzyme E2W (putative) 7.36

UBQLNL ubiquilin‐like 16.96

UCHL1 ubiquitin carboxyl‐terminal esterase L1 (ubiquitin thiolesterase) 44.44

UGT2B15 UDP glucuronosyltransferase 2 family, polypeptide B15 27.32

UGT2B17 UDP glucuronosyltransferase 2 family, polypeptide B17 19.99

USHBP1 Usher syndrome 1C binding protein 1 16.75

VRTN Vertebrae Development Homolog 2.16

WFIKKN1 WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain

containing 1

12.80

WNT10A wingless‐type MMTV integration site family, member 10A 189.62

WTH3DI RAB6C‐like 3.40

ZAP70 zeta‐chain (TCR) associated protein kinase 70kDa 33.22

ZCCHC12 zinc finger, CCHC domain containing 12 24.72


ZDHHC22 zinc finger, DHHC‐type containing 22 41.79

ZFHX4 zinc finger homeobox 4 27.12

ZFP2 zinc finger protein 2 homolog (mouse) 104.71

ZFR2 zinc finger RNA binding protein 2 43.64

ZNF438 zinc finger protein 438 14.83




ZNF674 zinc finger family member 674 2.05

ZP3 zona pellucida glycoprotein 3 (sperm receptor) 2.84

ZSCAN30 zinc finger and SCAN domain containing 30 2.19

Down‐regulated genes following PBX3 overexpression

Gene Symbol Gene name Ratio

ACSBG1 acyl‐CoA synthetase bubblegum family member 1 0.272

ACSM3 acyl‐CoA synthetase medium‐chain family member 3 0.024

ACTL8 actin‐like 8 0.472

ADAM8 ADAM metallopeptidase domain 8 0.106

ADAMTSL2 similar to ADAMTS‐like 2; ADAMTS‐like 2 0.398

ADAP1 ArfGAP with dual PH domains 1 0.452


ADC arginine decarboxylase 0.040

ADD3 adducin 3 (gamma) 0.265

ADRA1D adrenergic, alpha‐1D‐, receptor 0.005

AIM2 absent in melanoma 2 0.052

AIRE autoimmune regulator 0.019

AMACR C1q and tumor necrosis factor related protein 3;

alpha‐methylacyl‐CoA racemase 0.072

AMMECR1 Alport syndrome, mental retardation, midface hypoplasia and

elliptocytosis chromosomal region gene 1 0.110



AP3B2 adaptor‐related protein complex 3, beta 2 subunit 0.257

APOF apolipoprotein F 0.046

APOL3 apolipoprotein L, 3 0.130


APOM apolipoprotein M 0.375

AREG amphiregulin; amphiregulin B 0.483

ARID3C AT rich interactive domain 3C (BRIGHT‐like) 0.036

ARMCX2 armadillo repeat containing, X‐linked 2 0.080

ARRB1 arrestin, beta 1 0.356

ASB14 ankyrin repeat and SOCS box‐containing 14 0.099

ATP2A1 ATPase, Ca++ transporting, cardiac muscle, fast twitch 1 0.092

ATP5J2‐PTCD1 ATP5J2‐PTCD1 Read‐Through Transcript 0.105

ATP5SL ATP5S‐like 0.073

ATP8B4 ATPase, class I, type 8B, member 4 0.090


BCMO1 beta‐carotene 15,15'‐monooxygenase 1 0.008

BDH1 3‐hydroxybutyrate dehydrogenase, type 1 0.324

BST1 bone marrow stromal cell antigen 1 0.048

BST2 NPC‐A‐7; bone marrow stromal cell antigen 2 0.444

BTBD16 BTB (POZ) domain containing 16 0.048

BTBD18 hypothetical protein LOC643376 0.061

BTC betacellulin 0.034


















CAPS calcyphosine 0.469

CAPZB capping protein (actin filament) muscle Z‐line, beta 0.465

CCBL1 cysteine conjugate‐beta lyase, cytoplasmic 0.424


CCDC42B coiled‐coil domain containing 42B 0.443

CCL17 chemokine (C‐C motif) ligand 17 0.005

CCR3 chemokine (C‐C motif) receptor 3 0.004

CCR4 chemokine (C‐C motif) receptor 4 0.006





CDC45 CDC45 cell division cycle 45‐like (S. cerevisiae) 0.269

CDH22 cadherin‐like 22 0.085

CDKL4 cyclin‐dependent kinase‐like 4 0.008

CELF6 bruno‐like 6, RNA binding protein (Drosophila) 0.046

CFH complement factor H 0.042

CFI complement factor I 0.325

CFP complement factor properdin 0.032

CGREF1 cell growth regulator with EF‐hand domain 1 0.457

CHADL chondroadherin‐like 0.441

CHGA chromogranin A (parathyroid secretory protein 1) 0.009

CHRNB2 cholinergic receptor, nicotinic, beta 2 (neuronal) 0.416

CLCN2 chloride channel 2 0.062

CLEC3B C‐type lectin domain family 3, member B 0.418

CNGA1 cyclic nucleotide gated channel alpha 1 0.055

COL11A2 collagen, type XI, alpha 2 0.044

CORO7‐PAM16 CORO7‐PAM16 Read‐Through Transcript 0.094

CORT cortistatin; apoptosis‐inducing, TAF9‐like domain 1 0.331

CTRC chymotrypsin C (caldecrin) 0.024

CXCL11 chemokine (C‐X‐C motif) ligand 11 0.071


CXCR6 chemokine (C‐X‐C motif) receptor 6 0.241

CXorf56 chromosome X open reading frame 56 0.057

CYBB cytochrome b‐245, beta polypeptide 0.416



DCLK1 doublecortin‐like kinase 1 0.357

DENND2D DENN/MADD domain containing 2D 0.038

DES desmin 0.228

DLK1 delta‐like 1 homolog (Drosophila) 0.009

DNAH3 dynein, axonemal, heavy chain 3 0.120

DNAJB8 DnaJ (Hsp40) homolog, subfamily B, member 8 0.012

DOK1 docking protein 1‐like protein; docking protein 1, 62kDa

(downstream of tyrosine kinase 1) 0.388

DPEP2 dipeptidase 2 0.005

DPPA2 developmental pluripotency associated 2 0.011

DPT dermatopontin 0.035

DPYSL5 dihydropyrimidinase‐like 5 0.054

DRP2 dystrophin related protein 2 0.067

DTX3L deltex 3‐like (Drosophila) 0.391

DYDC1 DPY30 domain containing 1 0.039

EFCAB5 EF‐hand calcium binding domain 5 0.038

EFTUD2 elongation factor Tu GTP binding domain containing 2 0.449

EIF2AK2 eukaryotic translation initiation factor 2‐alpha kinase 2 0.433

EIF3CL eukaryotic translation initiation factor 3, subunit C‐like 0.076

EIF4A1

similar to eukaryotic translation initiation factor 4A; small nucleolar

RNA, H/ACA box 67; eukaryotic translation initiation factor 4A,

isoform 1

0.352

ELAC2 elaC homolog 2 (E. coli) 0.383

EPB41L3 erythrocyte membrane protein band 4.1‐like 3 0.052

EPHA4 EPH receptor A4 0.055

ERAP2 endoplasmic reticulum aminopeptidase 2 0.080

ERN2 endoplasmic reticulum to nucleus signaling 2 0.019

F2RL3 coagulation factor II (thrombin) receptor‐like 3 0.360

FABP4 fatty acid binding protein 4, adipocyte 0.080









FCER1G Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide 0.312

FCGRT Fc fragment of IgG, receptor, transporter, alpha 0.059

FIGF c‐fos induced growth factor (vascular endothelial growth factor D) 0.028

FOXR1 forkhead box R1 0.009

FRMD5 FERM domain containing 5 0.341


FZD10 frizzled homolog 10 (Drosophila) 0.385

FZD9 frizzled homolog 9 (Drosophila) 0.422


GABRR2 gamma‐aminobutyric acid (GABA) receptor, rho 2 0.031

GBP5 guanylate binding protein 5 0.068

GCNT7 glucosaminyl (N‐acetyl) transferase family member 7 0.367

GFAP glial fibrillary acidic protein 0.087

GFOD1 glucose‐fructose oxidoreductase domain containing 1 0.499

GIPC2 GIPC PDZ domain containing family, member 2 0.382

GLRB glycine receptor, beta 0.089

GMPR guanosine monophosphate reductase 0.136

GOLGA6A

golgi autoantigen, golgin subfamily a, 6C; golgi autoantigen, golgin

subfamily a, 6 pseudogene; golgi autoantigen, golgin subfamily a, 6D;

golgi autoantigen, golgin subfamily a, 6

0.061

GOLT1A golgi transport 1 homolog A (S. cerevisiae) 0.063

GPN1 GPN‐loop GTPase 1 0.069


GPR37 G protein‐coupled receptor 37 (endothelin receptor type B‐like) 0.042



GPRIN2 G protein regulated inducer of neurite outgrowth 2 0.007

GRAP2 GRB2‐related adaptor protein 2 0.156

HBE1 hemoglobin, epsilon 1 0.362

HBQ1 hemoglobin, theta 1 0.022

HERC6 hect domain and RLD 6 0.226

HES5 hairy and enhancer of split 5 (Drosophila) 0.025

HIPK4 homeodomain interacting protein kinase 4 0.022

HIST1H1A histone cluster 1, H1a 0.031

HIST1H2AH

histone cluster 1, H2ag; histone cluster 1, H2ah; histone cluster 1,

H2ai; histone cluster 1, H2ak; histone cluster 1, H2al; histone cluster

1, H2am

0.449

HIST1H2BL histone cluster 1, H2bl 0.173

HIST4H4

histone cluster 1, H4l; histone cluster 1, H4k; histone cluster 4, H4;

histone cluster 1, H4h; histone cluster 1, H4j; histone cluster 1, H4i;

histone cluster 1, H4d; histone cluster 1, H4c; histone cluster 1, H4f;

histone cluster 1, H4e; histone cluster 1, H4b; histone cluster 1, H4a;

histone cluster 2, H4a; histone cluster 2, H4b

0.376

HMP19 HMP19 protein 0.084



HPGD hydroxyprostaglandin dehydrogenase 15‐(NAD) 0.196

HPN hepsin 0.023

HRASLS2 HRAS‐like suppressor 2 0.021

HSH2D hematopoietic SH2 domain containing 0.210

HSPB9 heat shock protein, alpha‐crystallin‐related, B9 0.016

HYAL4 hyaluronoglucosaminidase 4 0.013

IFI35 interferon‐induced protein 35 0.371

IFIH1 interferon induced with helicase C domain 1 0.331

IFIT1 interferon‐induced protein with tetratricopeptide repeats 1 0.160



IFITM1 interferon induced transmembrane protein 1 (9‐27) 0.143

IFITM3 interferon induced transmembrane protein 3 (1‐8U) 0.459

IFNW1 interferon, omega 1 0.007

IGJ immunoglobulin J polypeptide, linker protein for immunoglobulin

alpha and mu polypeptides 0.008

IGSF6 immunoglobulin superfamily, member 6 0.036

IL13RA2 interleukin 13 receptor, alpha 2 0.384

IL17RE interleukin 17 receptor E 0.069

IL34 interleukin 34 0.496

IL6 interleukin 6 (interferon, beta 2) 0.343

IRF5 interferon regulatory factor 5 0.066

IRGC immunity‐related GTPase family, cinema 0.312

ITIH5 inter‐alpha (globulin) inhibitor H5 0.082

ITK IL2‐inducible T‐cell kinase 0.017


KCNRG potassium channel regulator 0.055

KIAA0232 KIAA0232 0.441

KIAA1107 KIAA1107 0.407

KIF5A kinesin family member 5A 0.177


KLRC4 killer cell lectin‐like receptor subfamily C, member 4 0.034

KLRC4‐KLRK1 KLRC4‐KLRK1 Read‐Through Transcript 0.042

KLRD1 killer cell lectin‐like receptor subfamily D, member 1 0.103


LAMP3 lysosomal‐associated membrane protein 3 0.298

LAP3 leucine aminopeptidase 3 0.432

LAT linker for activation of T cells 0.478

LCLAT1 lysocardiolipin acyltransferase 1 0.454

LCN10 lipocalin 10 0.006

LDB3 LIM domain binding 3 0.101

LGALS2 lectin, galactoside‐binding, soluble, 2 0.483

LMAN2L lectin, mannose‐binding 2‐like 0.047

LOC100505676 0.038

LOC100507003 0.059

LOC729020 rcRPE; ribulose‐5‐phosphate‐3‐epimerase 0.057

LPHN1 latrophilin 1 0.447


LRP1B low density lipoprotein‐related protein 1B (deleted in tumors) 0.089


LRRD1 Leucine‐rich repeat and death domain‐containing protein 1 0.012

MAK male germ cell‐associated kinase 0.116

MAP1LC3A microtubule‐associated protein 1 light chain 3 alpha 0.044

MARK2 MAP/microtubule affinity‐regulating kinase 2 0.486

MDFI MyoD family inhibitor 0.006

MDK midkine (neurite growth‐promoting factor 2) 0.442

MEFV Mediterranean fever 0.043

MIP major intrinsic protein of lens fiber 0.079

MMRN1 multimerin 1 0.027

MSH4 mutS homolog 4 (E. coli) 0.025

MT1F metallothionein 1F 0.014

MTRNR2L7 MTRNR2‐Like 7 0.059

MUC2 mucin 2, oligomeric mucus/gel‐forming 0.139

MUC5B mucin 5B, oligomeric mucus/gel‐forming 0.105

MX1 myxovirus (influenza virus) resistance 1, interferon‐inducible protein

p78 (mouse) 0.461

MXRA8 matrix‐remodelling associated 8 0.485

MYBPH myosin binding protein H 0.014

MYBPHL myosin binding protein H‐like 0.010

MYO9B myosin IXB 0.342

NAALAD2 N‐acetylated alpha‐linked acidic dipeptidase 2 0.254

NCCRP1 non‐specific cytotoxic cell receptor protein 1 homolog (zebrafish) 0.048

NCF2 neutrophil cytosolic factor 2 0.083

NIPAL2 NIPA‐like domain containing 2 0.204

NMB neuromedin B 0.036

NME5 non‐metastatic cells 5, protein expressed in (nucleoside‐diphosphate

kinase) 0.009

NPFF neuropeptide FF‐amide peptide precursor 0.406

NR0B2 nuclear receptor subfamily 0, group B, member 2 0.010

NR1D2 nuclear receptor subfamily 1, group D, member 2 0.077


NT5C1B‐RDH14 NT5C1B‐RDH14 Read‐Through Transcript 0.092

OAS1 2',5'‐oligoadenylate synthetase 1, 40/46kDa 0.319

OAS3 2'‐5'‐oligoadenylate synthetase 3, 100kDa 0.264

OR51B4 olfactory receptor, family 51, subfamily B, member 4 0.005

OR51B5 olfactory receptor, family 51, subfamily B, member 5 0.024

OR52N4 olfactory receptor, family 52, subfamily N, member 4 0.006

OR7E24 olfactory receptor, family 7, subfamily E, member 24 0.054

OTX1 orthodenticle homeobox 1 0.430

P2RY4 pyrimidinergic receptor P2Y, G‐protein coupled, 4 0.009

PABPC4L poly(A) binding protein, cytoplasmic 4‐like 0.005

PADI4 peptidyl arginine deiminase, type IV 0.016

PARD3B par‐3 partitioning defective 3 homolog B (C. elegans) 0.091

PARP10 poly (ADP‐ribose) polymerase family, member 10 0.492




PCDHB16 protocadherin beta 16 0.209



PCDHGA1 protocadherin gamma subfamily A, 1 0.036




PCDHGB2 protocadherin gamma subfamily B, 2 0.052

PCDHGB7 protocadherin gamma subfamily B, 7 0.365

PCSK5 proprotein convertase subtilisin/kexin type 5 0.059


PDHB pyruvate dehydrogenase (lipoamide) beta 0.491

PELI3 pellino homolog 3 (Drosophila) 0.485

PGBD5 piggyBac transposable element derived 5 0.416

PGPEP1L pyroglutamyl‐peptidase 1‐like 0.042

PIK3AP1 phosphoinositide‐3‐kinase adaptor protein 1 0.394

PLSCR1 phospholipid scramblase 1 0.362

PLVAP plasmalemma vesicle associated protein 0.029

PMF1‐BGLAP PMF1‐BGLAP Read‐Through Transcript 0.457

PMFBP1 polyamine modulated factor 1 binding protein 1 0.408

PNPT1 polyribonucleotide nucleotidyltransferase 1 0.420

POC1B‐GALNT4 POC1B‐GALNT4 Read‐Through Transcript 0.122

POF1B premature ovarian failure, 1B 0.021

PPARD peroxisome proliferator‐activated receptor delta 0.411

PPP6C protein phosphatase 6, catalytic subunit 0.498

PRELP proline/arginine‐rich end leucine‐rich repeat protein 0.092

PRICKLE1 prickle homolog 1 (Drosophila) 0.056

PROX2 prospero homeobox 2 0.093

PRPH2 peripherin 2 (retinal degeneration, slow) 0.016

PRR24 hypothetical protein LOC255783 0.272

PRR5‐ARHGAP8 Rho GTPase activating protein 8; proline rich 5 (renal);

PRR5‐ARHGAP8 fusion 0.051

PRRG2 proline rich Gla (G‐carboxyglutamic acid) 2 0.278

PSMD1 proteasome (prosome, macropain) 26S subunit, non‐ATPase, 1 0.061

PSTPIP1 proline‐serine‐threonine phosphatase interacting protein 1 0.014

PTGDS prostaglandin D2 synthase, hematopoietic; prostaglandin D2

synthase 21kDa (brain) 0.035

PTPRB protein tyrosine phosphatase, receptor type, B 0.129

PTX4 chromosome 16 open reading frame 38 0.005

RAB17 RAB17, member RAS oncogene family 0.025

RAB9B RAB9B, member RAS oncogene family 0.020

RAET1G retinoic acid early transcript 1G 0.410


RAP1GDS1 RAP1, GTP‐GDP dissociation stimulator 1 0.497


RBP1 retinol binding protein 1, cellular 0.360

RIMBP3B RIMS binding protein 3B; RIMS binding protein 3C; RIMS binding

protein 3 0.132

RIMBP3C RIMS binding protein 3B; RIMS binding protein 3C; RIMS binding

protein 3 0.328


RPRM reprimo, TP53 dependent G2 arrest mediator candidate 0.008019

RSAD2 radical S‐adenosyl methionine domain containing 2 0.196522

RUSC1‐AS1 RUSC1 antisense RNA 1 0.497053

SAMD5 sterile alpha motif domain containing 5 0.127803

SAMHD1 SAM domain and HD domain 1 0.328355

SAP25 Sin3A‐associated protein 0.397751

SCRT1 scratch homolog 1, zinc finger protein (Drosophila) 0.02862

SDHD

similar to succinate dehydrogenase complex, subunit D, integral

membrane protein; succinate dehydrogenase complex, subunit D,

integral membrane protein

0.060534

SECTM1 secreted and transmembrane 1 0.431267

SEMA6A sema domain, transmembrane domain (TM), and cytoplasmic

domain, (semaphorin) 6A 0.488318

SERPINB10 serpin peptidase inhibitor, clade B (ovalbumin), member 10 0.017739

SERPINB2 serpin peptidase inhibitor, clade B (ovalbumin), member 2 0.460325

SFI1 Sfi1 homolog, spindle assembly associated (yeast) 0.453148

SGPP2 sphingosine‐1‐phosphate phosphotase 2 0.034786

SHBG sex hormone‐binding globulin 0.052575

SHMT2 serine hydroxymethyltransferase 2 (mitochondrial) 0.042054

SIDT1 SID1 transmembrane family, member 1 0.009828

SLC10A1 solute carrier family 10 (sodium/bile acid cotransporter family),

member 1 0.007138

SLC25A13 solute carrier family 25, member 13 (citrin) 0.300565




SLC7A7 solute carrier family 7 (cationic amino acid transporter, y+ system),

member 7 0.088014


member 8 0.075226

SLCO1C1 solute carrier organic anion transporter family, member 1C1 0.040872

SLFN11 schlafen family member 11 0.251936

SLFNL1 schlafen‐like 1 0.434731

SMPDL3B sphingomyelin phosphodiesterase, acid‐like 3B 0.011364

SP110 SP110 nuclear body protein 0.044318

SPRED3 sprouty‐related, EVH1 domain containing 3 0.041259

SRL sarcalumenin 0.480133

ST18 suppression of tumorigenicity 18 (breast carcinoma) (zinc finger 0.01131

protein)

ST3GAL5 ST3 beta‐galactoside alpha‐2,3‐sialyltransferase 5 0.436894


ST8SIA5 ST8 alpha‐N‐acetyl‐neuraminide alpha‐2,8‐sialyltransferase 5 0.040193

STOML1 stomatin (EPB72)‐like 1 0.042074

STOX1 storkhead box 1 0.479429

STX19 syntaxin 19 0.060201

STXBP2 syntaxin binding protein 2 0.43449

STXBP5L8 syntaxin binding protein 5‐like 0.169636

SYNJ2BP‐COX16 SYNJ2BP‐COX16 Read‐Through Transcript 0.038542

SYNPO2 synaptopodin 2 0.450861

TAL2 T‐cell acute lymphocytic leukemia 2 0.024599


TBC1D28 TBC1 domain family, member 28 0.014994

TBC1D29 TBC1 domain family, member 29 0.007344

TBRG4 transforming growth factor beta regulator 4 0.464622

TCTE1 t‐complex‐associated‐testis‐expressed 1 0.009037

TEX19 testis expressed 19 0.482793

TGIF2‐C20ORF24 TGIF2‐C20ORF24 Read‐Through Transcript 0.032766

THTPA thiamine triphosphatase 0.46625


TMC6 transmembrane channel‐like 6 0.468143

TMEM14E transmembrane protein 14E 0.006931

TMEM183B transmembrane protein 183A; transmembrane protein 183B 0.392782

TMEM229B chromosome 14 open reading frame 83 0.455182

TMEM232 hypothetical protein LOC642987 0.474396


TMPRSS6 transmembrane protease, serine 6 0.306026

TNFAIP8L2 tumor necrosis factor, alpha‐induced protein 8‐like 2 0.019201

TNFRSF8 tumor necrosis factor receptor superfamily, member 8 0.054544

TNFSF10 tumor necrosis factor (ligand) superfamily, member 10 0.467522

TNNI3 troponin I type 3 (cardiac) 0.017875

TOMM40 translocase of outer mitochondrial membrane 40 homolog (yeast) 0.407491

TPTE transmembrane phosphatase with tensin homology 0.065192

TRAF3IP1 TNF receptor‐associated factor 3 interacting protein 1 0.47951

TRANK1 lupus brain antigen 1 0.238881




TRIM34 TRIM6‐TRIM34 readthrough transcript; tripartite motif‐containing 6;

tripartite motif‐containing 34 0.341296


TRIML1 tripartite motif family‐like 1 0.381682

TSN translin 0.461096

TTC23L tetratricopeptide repeat domain 23‐like 0.007338

TUBA3D tubulin, alpha 3d; tubulin, alpha 3c 0.379318

U2AF1L4 U2 small nuclear RNA auxiliary factor 1‐like 4 0.473631

UBA7 ubiquitin‐like modifier activating enzyme 7 0.261071

ULK2 unc‐51‐like kinase 2 (C. elegans) 0.289878

UNC5D unc‐5 homolog D (C. elegans) 0.039076

USH1G Usher syndrome 1G (autosomal recessive) 0.019104

USP18 ubiquitin specific peptidase 18 0.317838

UXT ubiquitously‐expressed transcript 0.439903

VMO1 vitelline membrane outer layer 1 homolog (chicken) 0.01623

VTN vitronectin 0.21341

WDR86 WD repeat domain 86 0.380295



WNT2B wingless‐type MMTV integration site family, member 2B 0.032417

XYLT1 xylosyltransferase I 0.113656

YTHDF2 YTH domain family, member 2 0.470145

ZBTB32 zinc finger and BTB domain containing 32 0.44698

ZC4H2 zinc finger, C4H2 domain containing 0.055356

ZFAT zinc finger and AT hook domain containing 0.444769

ZKSCAN5 zinc finger with KRAB and SCAN domains 5 0.447756











ZNF878 similar to zinc finger protein 709 0.03129

ZPLD1 zona pellucida‐like domain containing 1 0.027586

Supplementary Table 6. GO analysis of different expression genes after PBX3‐overexpression by DAVID database via

biological process terms

Term Count % PValue Genes

Cell surface

receptor linked

signal

transduction

98 11.34 3.2E‐02

F2RL3, ADCY2, OR4F21, GRIK2, LHCGR, CXCL11, MARCO,

LPHN3, APOA1, GAB2, ELTD1, PDGFC, CIB2, ADAM8, ROS1,

KLRD1, LPHN1, WNT10A, FGF22, GEM, THY1, IGSF6,

GABRR2, CCR4, CCR3, ITGAL, IFITM1, HMP19, ITGBL1,

ADAP1, OR52N4, P2RY4, TEK, OR51B5, ZAP70, FCER1G,

OR51B4, KLRF1, GPR20, ANGPTL3, PLAT, GPR158,

TNFRSF13B, KCNK2, NPY5R, NOTCH3, SEMA6A, GNGT1,

EPHA4, LAT, EMR1, GPR37, NPW, OR6K3, CD79A, AREG,

CORT, LHB, ADRA1D, GPR84, GPR85, TAS2R5, LEPR, TACR1,

GNRHR, GABBR2, OR7E24, SCT, CXCR5, OR13A1, CXCR6,

NOS3, APLN, NPFF, GPR97, GPR176, DOK1, PTAFR, NKD2,

FFAR1, ABI1, NMB, SCG5, FIGF, CD7, FZD9, COL4A3, PTPRC,

GLRB, PTPRE, DGKI, CISH, CCL17, WNT2B, FZD10, TAS2R30,

HPGD, CD14

Immune response 63 7.29 4.5E‐08

TLR3, BNIP3, VTN, CXCL11, TLR9, CFP, RAET1G, IL1RAP,

TICAM2, CFH, ERAP2, CFI, APLN, LAIR1, GBP5, BST2, NCF2,

BST1, STXBP2, YTHDF2, GEM, CNGA1, SIGIRR, CTSW, IGSF6,

CCR4, TREM1, PTAFR, TNFAIP8L2, ITGAL, C7, IFIH1, IFITM3,

OAS3, RAG1, RSAD2, OAS1, FCGRT, CD70, RAG2, IFI35,

FCGR1A, ZAP70, HLA‐DRB4, FCER1G, C2, CD7, SECTM1,

PTPRC, IL6, TNFRSF13B, IGJ, SAMHD1, LOC554223, AIM2,

CD180, CCL17, LAT, TNFSF10, CYBB, AIRE, CD79A, CD14

Cell adhesion 54 6.25 6.3E‐05

CLDN7, PPARD, PCDHA9, MYBPC2, MYBPC3, PCDHGA6, VTN,

PCDHGA5, PCDHGA4, MMRN1, PCDHGA1, CDH22,

CNTNAP2, COL11A2, KIRREL2, ADAM8, BOC, NEGR1,

SPACA4, CLCA2, PCDHB8, PCDHB6, PCDHGB7, CPXM2,

PCDHGB2, BCL2L11, THY1, AMBP, HES5, CCR3, ITGAL,

PPFIA1, PKD1L1, SCARF2, ITGBL1, SEMA5A, LY6D, PCDHB16,

MYBPH, TEK, PSTPIP1, ANGPTL3, GPNMB, DPT, HAPLN2,

COL4A3, PTPRC, LGALS4, COL13A1, PRPH2, OMD, EMR1,

OMG, MUC5B

Ion transport 46 5.32 2.7E‐02

SLC5A2, KCNC1, CLCN2, GRIK2, SLC22A14, SLC22A11, KCNRG,

FKBP1B, KCNK12, KCNJ14, BEST4, MARCO, BEST2, KCNQ5,

KCNS1, SLCO1A2, P2RY4, ANO2, SLCO1C1, KCNE3, PTPRC,

CACNA2D1, CLCA2, GLRB, KCND2, SLC8A2, SCN2B, KCNB1,

AMACR, TOMM40, KCNK2, CNGA1, SLC10A1, GABRR2, CYBB,

SLC25A13, CLIC3, SLC6A8, P2RX3, ATP2A1, SLCO1B1,

CHRNB4, CHRNB2, ATP6V0A4, CHRNG, KCTD12

Cell‐cell signaling 45 5.21 5.2E‐04

DHH, CPLX3, GRIK2, SOX2, FFAR1, CD70, NMB, GABBR2,

CXCL11, FKBP1B, HOXD11, SEMA5A, KCNQ5, PCDHB16, TEK,

SYN2, PCSK5, NPFF, PLAT, STX1A, IL6, GLRB, GPR176, KCND2,

BST2, SCN2B, KIF5A, PCDHB6, PARK2, NPY5R, CCL17,

GABRR2, NAALAD2, ATXN3, TNFSF10, CAMK4, P2RX3,

CHRNB4, CHRNB2, AREG, GRAP2, CORT, LHB, ADRA1D,

NR5A1

Homeostatic

process 45 5.21 2.9E‐02

DHH, C7, PPARD, GRIK2, PDIA2, TACR1, FGGY, PRND, FFAR1,

SLC7A8, BNIP3, FKBP1B, ACSBG1, BEST2, APOA1, P2RY4,

HAAO, COL11A2, ANGPTL3, APOM, GAL3ST1, MB, CD7,

MUC2, PTPRC, IL6, GLRB, KCND2, TNFRSF13B, MTL5, TNNI3,

BCL2L11, GIMAP1, CD38, HIF1A, CCR4, CCR3, ATP2A1,

CHRNB4, FABP4, CHRNB2, LIPC, ATP6V0A4, NR5A2, CHRNG

Inflammatory

response 28 3.24 1.1E‐03

C7, ITGAL, TACR1, TLR3, CXCL11, TLR9, CFP, IL17D, MEFV,

IL1RAP, TICAM2, CFH, C2, CFI, IL6, CD180, CCL17, SIGIRR,

APOL3, CYBB, HIF1A, SERPINF2, CCR4, CCR3, CARD18,

ALOX5, CD14, PTAFR

Regulation of

system process 26 3.01 2.3E‐03

CPLX3, GRIK2, TACR1, BTC, MYBPC3, RPS6KB1, FKBP1B,

APOA1, DES, MYBPH, NOS3, PLAT, STX1A, NTF4, PARK2,

TNNI3, NPY5R, CD38, P2RX3, HSPB7, ATP2A1, CHRNB4,

CHRNB2, ALOX5, PBX3, ADRA1D

Regulation of

hydrolase activity 22 2.55 6.5E‐02

FGD2, TBC1D3C, COL4A3, F2RL3, LEPR, TACR1, MYBPC3,

LHCGR, RAG1, TNNI3, FKBP1B, ADAP1, THY1, APOA1, ADAP2,

TBC1D29, P2RY4, TBC1D28, NOS3, CSTA, ANGPTL3, FGD5

Steroid metabolic

process 18 2.08 7.4E‐03

PPARD, CYP11A1, LEPR, PRKAG2, AMACR, DHRS9, NR0B2,

UGT2B17, CYP39A1, APOA1, AKR1B15, APOF, SULT1A2,

UGT2B15, NR5A2, ANGPTL3, LIPC, LHB

Fatty acid

metabolic process 16 1.85 2.7E‐02

PPARD, ALOXE3, ACSM2A, PRKAG2, ACSBG1, ACSM3,

PRKAR2B, PTGDS, ALOX12B, FABP4, ELOVL7, ALOX5, LIPC,

ANGPTL3, HPGD, ACSL6

Regulation of

membrane

potential

14 1.62 5.8E‐03DHH, GLRB, PPARD, KCND2, GRIK2, TACR1, BNIP3, GIMAP1,

ACSBG1, BEST2, CHRNB4, CHRNB2, GAL3ST1, CHRNG

Response to

hypoxia 12 1.39 3.3E‐02

PLAT, CD38, NOL3, HIF1A, CA9, PDIA2, P2RX3, ALDOC, BNIP3,

NOS3, CHRNB2, MB

Supplementary Table 7. Embryo development associated genes up‐regulated by PBX3 DAVID ID Gene name RatioA1BG alpha-1-B glycoprotein 41.51 ABHD1 abhydrolase domain containing 1 2.83 ACOT6 acyl-CoA thioesterase 6 2.64 ACSL6 acyl-CoA synthetase long-chain family member 6 8.24 ACSM2A acyl-CoA synthetase medium-chain family member 2A 67.83 ADCY2 adenylate cyclase 2 (brain) 30.73 AHSP erythroid associated factor 476.19 ALOX5 arachidonate 5-lipoxygenase 16.66 ALOXE3 arachidonate lipoxygenase 3 28.09 AMBP alpha-1-microglobulin/bikunin precursor 2.19 AMN amnionless homolog (mouse) 32.11 ANGPTL3 angiopoietin-like 3 254.27 ANK2 ankyrin 2, neuronal 16.88 ANKRD45 ankyrin repeat domain 45 19.49 APCDD1L adenomatosis polyposis coli down-regulated 1-like 29.48 APLN apelin 2.47 APOA1 apolipoprotein A-I 41.18

APOBEC2 apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 2

40.57

ARHGAP15

Rho GTPase activating protein 15 19.52

ARHGAP19

Rho GTPase activating protein 19 11.40

ASGR1 asialoglycoprotein receptor 1 37.87 ASPN asporin 79.26 ATP6V0A4

ATPase, H+ transporting, lysosomal V0 subunit a4 29.29

BCL2L14 BCL2-like 14 (apoptosis facilitator) 98.77 BCL2L2 BCL2-like 2 2.14 BEST2 bestrophin 2 148.04 BEST4 bestrophin 4 2.90 BMP5 bone morphogenetic protein 5 10.17 BOC Boc homolog (mouse) 17.75 C11orf16 chromosome 11 open reading frame 16 18.00 C1orf228 chromosome 1 open reading frame 228 2.04 C2orf72 chromosome 2 open reading frame 72 34.96 C8orf74 chromosome 8 open reading frame 74 294.85 C9orf50 chromosome 9 open reading frame 50 151.89 CACNA2D1

calcium channel, voltage-dependent, alpha 2/delta subunit 1 2884.7

9 CAMK4 calcium/calmodulin-dependent protein kinase IV 11.77 CAPN5 calpain 5 4.75

CARD18 caspase recruitment domain family, member 18 14.45 CASC1 cancer susceptibility candidate 1 26.48 CCDC122 coiled-coil domain containing 122 2.66 CCDC149 coiled-coil domain containing 149 3.37 CCDC17 coiled-coil domain containing 17 15.76 CCDC33 coiled-coil domain containing 33 37.22 CCDC62 coiled-coil domain containing 62 2.58 CEACAM19

carcinoembryonic antigen-related cell adhesion molecule 19 15.11

CHD5 chromodomain helicase DNA binding protein 5 2.26 CHRNG cholinergic receptor, nicotinic, gamma 32.30 CIB2 calcium and integrin binding family member 2 27.21 CLGN calmegin 2.11 CLIC3 chloride intracellular channel 3 2.52 CLIP3 CAP-GLY domain containing linker protein 3 2.81 CNIH3 cornichon homolog 3 (Drosophila) 19.49 COL4A3 collagen, type IV, alpha 3 (Goodpasture antigen) 4.81 CPLX3 complexin 3 71.78 CRYGS crystallin, gamma S 47.87 CYP39A1 cytochrome P450, family 39, subfamily A, polypeptide 1 2.86 CYP8B1 cytochrome P450, family 8, subfamily B, polypeptide 1 50.99 DBNDD1 dysbindin (dystrobrevin binding protein 1) domain containing 1 17.44 DHH desert hedgehog homolog (Drosophila) 27.78 DIRAS1 DIRAS family, GTP-binding RAS-like 1 7.16 DNAJB5 DnaJ (Hsp40) homolog, subfamily B, member 5 2.25 DNAJC28 DnaJ (Hsp40) homolog, subfamily C, member 28 2.23 DNALI1 dynein, axonemal, light intermediate chain 1 22.53 DPPA4 developmental pluripotency associated 4 11.40 DSE dermatan sulfate epimerase 2.70 EGFL8 EGF-like-domain, multiple 8 2.44 EIF4ENIF1

eukaryotic translation initiation factor 4E nuclear import factor 1

2.10

ELAVL3 ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)

30.49

EMILIN3 elastin microfibril interfacer 3 2.95

EMR1 egf-like module containing, mucin-like, hormone receptor-like 1

12.87

ENPP7 ectonucleotide pyrophosphatase/phosphodiesterase 7 32.87

ESF1 similar to ABT1-associated protein; ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)

11.30

FAM109B family with sequence similarity 109, member B 13.31 FAM117A family with sequence similarity 117, member A 3.84 FAM180A family with sequence similarity 180, member A 282.44 FAM19A3 family with sequence similarity 19 (chemokine (C-C 24.31

motif)-like), member A3 FAM25C family with sequence similarity 25, member C 300.60 FAM92B family with sequence similarity 92, member B 106.17 FBLN2 fibulin 2 19.19 FCGR1A Fc fragment of IgG, high affinity Ia, receptor (CD64) 13.19 FER1L5 fer-1-like 5 (C. elegans) 25.03 FGD5 FYVE, RhoGEF and PH domain containing 5 108.00 FGGY FGGY carbohydrate kinase domain containing 32.46 FLG2 filaggrin family member 2 10.52 FLJ22184 hypothetical protein FLJ22184 2.25 FOXD4L1 forkhead box D4-like 1 40.44 FOXS1 forkhead box S1 148.86 FSIP2 fibrous sheath interacting protein 2 13.29 GABBR2 gamma-aminobutyric acid (GABA) B receptor, 2 8.50 GAL3ST1 galactose-3-O-sulfotransferase 1 128.88 GLIS1 GLIS family zinc finger 1 21.91 GNRHR gonadotropin-releasing hormone receptor 9.92 GOLGA6D

golgi autoantigen, golgin subfamily a, 6D 12.41

GPIHBP1 glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1

19.81

GPR176 G protein-coupled receptor 176 12.62 GPR85 G protein-coupled receptor 85 29.09 GRIK2 glutamate receptor, ionotropic, kainate 2 4.20 GRIP2 glutamate receptor interacting protein 2 2.75 GSTA2 glutathione S-transferase alpha 2 152.58 HAAO 3-hydroxyanthranilate 3,4-dioxygenase 154.80 HIC1 hypermethylated in cancer 1 24.58 HIST1H3J histone cluster 1, H3j 2.00 HIST1H4A

histone cluster 1, H4b; histone cluster 1, H4a; 19.39

HOXD3 homeobox D3 2.29 HS3ST3B1 heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1 2.05 IL1RAP interleukin 1 receptor accessory protein 33.89 INSM2 insulinoma-associated 2 13.90 IQUB IQ motif and ubiquitin domain containing 3.05 JAZF1 JAZF zinc finger 1 21.97 KATNAL1 katanin p60 subunit A-like 1 2.63

KCNB1 potassium voltage-gated channel, Shab-related subfamily, member 1

131.34

KCNC1 potassium voltage-gated channel, Shaw-related subfamily, member 1

43.60

KCNJ14 potassium inwardly-rectifying channel, subfamily J, member 14 2.12 KCNK2 potassium channel, subfamily K, member 2 19.87

KCNQ5 potassium voltage-gated channel, KQT-like subfamily, member 5

11.18

KIAA1045 KIAA1045 15.08 KIAA1683 KIAA1683 2.34 KIF26B kinesin family member 26B 19.26 KLHL32 kelch-like 32 (Drosophila) 6.06 KLRF1 killer cell lectin-like receptor subfamily F, member 1 40.41 KRT32 keratin 32 426.17 LEPR leptin receptor 15.92 LHB luteinizing hormone beta polypeptide 25.42 LHCGR luteinizing hormone/choriogonadotropin receptor 14.78 LIN28A lin-28 homolog (C. elegans) 10.45 LOC554223

hypothetical LOC554223 86.05

LOC728392

hypothetical protein LOC728392 2.75

LRRC17 leucine rich repeat containing 17 14.84 LRRC39 leucine rich repeat containing 39 20.81

MAF v-maf musculoaponeurotic fibrosarcoma oncogene homolog (avian)

47.09

MAGI2 membrane associated guanylate kinase, WW and PDZ domain containing 2

4.51

MAT1A methionine adenosyltransferase I, alpha 28.12 MED12L mediator complex subunit 12-like 4.51 MFSD2B hypothetical protein LOC388931 163.57 MSI1 musashi homolog 1 (Drosophila) 67.82 MTL5 metallothionein-like 5, testis-specific (tesmin) 3.79 MYBPC2 myosin binding protein C, fast type 39.58 MYBPC3 myosin binding protein C, cardiac 3.24 MYLK3 myosin light chain kinase 3 2.67 MYO1A myosin IA 13.60 MYOZ1 myozenin 1 53.69 NEGR1 neuronal growth regulator 1 3.43 NKD2 naked cuticle homolog 2 (Drosophila) 14.87 NOTCH3 Notch homolog 3 (Drosophila) 17.18 NOVA2 neuro-oncological ventral antigen 2 185.06

NPL N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)

11.92

NPW neuropeptide W 2.16 NPY5R neuropeptide Y receptor Y5 73.56 NR5A1 nuclear receptor subfamily 5, group A, member 1 14.78 NR5A2 nuclear receptor subfamily 5, group A, member 2 30.12 NTF4 neurotrophin 4 450.80 NYNRIN KIAA1305 38.45

ODAM odontogenic, ameloblast asssociated 55.84 OLFM2 olfactomedin 2 29.83 OMD osteomodulin 112.05 OMG oligodendrocyte myelin glycoprotein 2.07 P2RX3 purinergic receptor P2X, ligand-gated ion channel, 3 60.93 P4HA1 prolyl 4-hydroxylase, alpha polypeptide I 8.17 PALM3 Paralemmin-3 50.43 PAPPA2 pappalysin 2 46.30 PBX3 pre-B-cell leukemia homeobox 3 88.94 PCDHA9 protocadherin alpha 9 2.16 PCOLCE procollagen C-endopeptidase enhancer 211.29 PDIA2 protein disulfide isomerase family A, member 2 233.37 PDLIM4 PDZ and LIM domain 4 19.77 PKD1L1 polycystic kidney disease 1 like 1 14.95 PLA2G4D phospholipase A2, group IVD (cytosolic) 130.30 PLAG1 pleiomorphic adenoma gene 1 18.21 PLXNA4 plexin A4 39.31

PPFIA4 protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4

4.41

PPP1R1C protein phosphatase 1, regulatory (inhibitor) subunit 1C 223.65 PRKAR2B protein kinase, cAMP-dependent, regulatory, type II, beta 35.87 PRND prion protein 2 (dublet) 2.52 PTPRR protein tyrosine phosphatase, receptor type, R 54.15 RAG1 recombination activating gene 1 3.74 RAPGEF5 Rap guanine nucleotide exchange factor (GEF) 5 30.38

RBPJL recombination signal binding protein for immunoglobulin kappa J region-like

27.77

RFESD Rieske (Fe-S) domain containing 2.48 RFX3 regulatory factor X, 3 (influences HLA class II expression) 23.46 RGAG1 retrotransposon gag domain containing 1 3.24 RGMA RGM domain family, member A 18.12 RNF182 ring finger protein 182 2.13 ROS1 c-ros oncogene 1 , receptor tyrosine kinase 2.11 RPS6KB1 ribosomal protein S6 kinase, 70kDa, polypeptide 1 2.21 RTDR1 rhabdoid tumor deletion region gene 1 39.71 SALL2 sal-like 2 (Drosophila) 6.24 SCARF2 scavenger receptor class F, member 2 12.00 SCG5 secretogranin V (7B2 protein) 36.45 SCGB1D2 secretoglobin, family 1D, member 2 627.37 SCN2B sodium channel, voltage-gated, type II, beta 8.43 SDC2 syndecan 2 6.96

SEMA5A sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A

2.44

SERPINC1

serpin peptidase inhibitor, clade C (antithrombin), member 1 31.09

SERPINF2

serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2

17.57

SGK2 serum/glucocorticoid regulated kinase 2 20.06 SGOL1 shugoshin-like 1 (S. pombe) 9.40 SHISA7 UPF0626 protein A 10.58 SIAH3 seven in absentia homolog 3 (Drosophila) 35.56

SLC22A11 solute carrier family 22 (organic anion/urate transporter), member 11

111.92

SLC22A14 solute carrier family 22, member 14 36.99 SLC43A1 solute carrier family 43, member 1 44.14 SLC8A2 solute carrier family 8 (sodium/calcium exchanger), member 2 32.53 SLCO1A2 solute carrier organic anion transporter family, member 1A2 7.14 SLCO1B1 solute carrier organic anion transporter family, member 1B1 101.72 SNX20 sorting nexin 20 43.10 SOX2 SRY (sex determining region Y)-box 2 3.74 SPACA4 sperm acrosome associated 4 26.29 SPTY2D1 SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae) 24.41

SULT1A2 sulfotransferase family, cytosolic, 1A, phenol-preferring, member 2

2.22


TAF7L TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa

16.89

TBC1D3C TBC1 domain family, member 3B; TBC1 domain family, member 3C

22.31

TEK TEK tyrosine kinase, endothelial 25.59 TMEM119 transmembrane protein 119 52.73 TMEM191C

transmembrane protein 191B; transmembrane protein 191C 34.32

TMEM63C

transmembrane protein 63C 2.34

TMEM88 transmembrane protein 88 34.92 TOX thymocyte selection-associated high mobility group box 168.89 TP53TG5 TP53 target 5 18.43 TRIM63 tripartite motif-containing 63 197.36 TRIM71 tripartite motif-containing 71 78.61 TSPAN5 tetraspanin 5 3.51 UBQLNL ubiquilin-like 16.96 UCHL1 ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) 44.44 UGT2B17 UDP glucuronosyltransferase 2 family, polypeptide B17 19.99

WFIKKN1 WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1

12.80

WNT10A wingless-type MMTV integration site family, member 10A 189.62

ZAP70 zeta-chain (TCR) associated protein kinase 70kDa 33.22 ZCCHC12 zinc finger, CCHC domain containing 12 24.72 ZDHHC22 zinc finger, DHHC-type containing 22 41.79 ZFHX4 zinc finger homeobox 4 27.12 ZFR2 zinc finger RNA binding protein 2 43.64 ZNF521 zinc finger protein 521 78.12 ZNF649 zinc finger protein 649 14.46

Supplementary Table 8. Genes directly regulated by PBX3 as revealed by RNA‐seq and ChIP‐seq

analysis

Gene symbol Gene name Ratio

Up‐regulated genes

ABCB1 ATP‐binding cassette, sub‐family B (MDR/TAP), member 1 3.89

ABI1 abl‐interactor 1 2.64

ADCY2 adenylate cyclase 2 (brain) 30.73

ADPGK ADP‐dependent glucokinase 31.65

ANK1 ankyrin 1, erythrocytic 10.05

ANK2 ankyrin 2, neuronal 16.88



ANO2 anoctamin 2 10.38



ARL17B ADP‐ribosylation factor‐like 17 pseudogene 1; ADP‐ribosylation

factor‐like 17 2.09

ARSD arylsulfatase D 27.50

ART1 ADP‐ribosyltransferase 1 150.86

ASPN asporin 79.26

ATF3 activating transcription factor 3 3.05

ATG9B ATG9 autophagy related 9 homolog B (S. cerevisiae) 2.67

ATP6V0A4 ATPase, H+ transporting, lysosomal V0 subunit a4 29.29

ATXN3 ataxin 3 2.16


BMP5 bone morphogenetic protein 5 10.17

BNIP3 BCL2/adenovirus E1B 19kDa interacting protein 3 3.65

BOC Boc homolog (mouse) 17.75









CACNA2D1 calcium channel, voltage‐dependent, alpha 2/delta subunit 1 2884.80

CAMK4 calcium/calmodulin‐dependent protein kinase IV 11.77

CASC1 cancer susceptibility candidate 1 26.48







CES3 carboxylesterase 3 9.76

CHD5 chromodomain helicase DNA binding protein 5 2.26

CIB2 calcium and integrin binding family member 2 27.21

CLGN calmegin 2.11

CLUL1 clusterin‐like 1 (retinal) 13.16

CNIH3 cornichon homolog 3 (Drosophila) 19.49

CNTNAP2 contactin associated protein‐like 2 3.05

COL13A1 collagen, type XIII, alpha 1 35.02

COL4A3 collagen, type IV, alpha 3 (Goodpasture antigen) 4.81

CPNE5 copine V 73.87

CPXM2 carboxypeptidase X (M14 family), member 2 3.41


DGKI diacylglycerol kinase, iota 9.37

DHRS9 dehydrogenase/reductase (SDR family) member 9 7.25

DIRAS1 DIRAS family, GTP‐binding RAS‐like 1 7.16

DSE dermatan sulfate epimerase 2.70

EFHD1 EF‐hand domain family, member D1 18.39

EIF4ENIF1 eukaryotic translation initiation factor 4E nuclear import factor 1 2.10

ELOVL7 ELOVL family member 7, elongation of long chain fatty acids (yeast) 2.24

ELTD1 EGF, latrophilin and seven transmembrane domain containing 1 17.58

ENKUR enkurin, TRPC channel interacting protein 34.55

EpCAM epithelial cell adhesion molecule 24.20

EPN2 epsin 2 2.88

ESF1 similar to ABT1‐associated protein; ESF1, nucleolar pre‐rRNA

processing protein, homolog (S. cerevisiae) 11.30

EYA2 eyes absent homolog 2 (Drosophila) 77.76


FAM196A chromosome 10 open reading frame 141 45.70


FBLN2 fibulin 2 19.19





FGGY FGGY carbohydrate kinase domain containing 32.46

FMN1 formin 1 15.46

FRK fyn‐related kinase 2.10

FRMPD4 FERM and PDZ domain containing 4 6.22

FSTL4 follistatin‐like 4 8.83

FUZ fuzzy homolog (Drosophila) 2.41



N‐acetylgalactosaminyltransferase 12 (GalNAc‐T12) 4.15


N‐acetylgalactosaminyltransferase 8 (GalNAc‐T8) 94.33

GEM GTP binding protein overexpressed in skeletal muscle 112.38

GLIS1 GLIS family zinc finger 1 21.91

GPA33 glycoprotein A33 (transmembrane) 22.00

GPNMB glycoprotein (transmembrane) nmb 2.25





GRAMD3 GRAM domain containing 3 2.13

GRIK2 glutamate receptor, ionotropic, kainate 2 4.20

GULP1 GULP, engulfment adaptor PTB domain containing 1 2.90

HIF1A hypoxia inducible factor 1, alpha subunit (basic helix‐loop‐helix

transcription factor) 16.95


HS3ST3B1 heparan sulfate (glucosamine) 3‐O‐sulfotransferase 3B1 2.05

IGFBP2 insulin‐like growth factor binding protein 2, 36kDa 197.93

IGFBP5 insulin‐like growth factor binding protein 5 14.42

IL17D interleukin 17D 3.58

IL1RAP interleukin 1 receptor accessory protein 33.89

INHBC inhibin, beta C 2.02

INMT indolethylamine N‐methyltransferase 13.90

ISPD notch1‐induced protein 3.24

ITGAL integrin, alpha L (antigen CD11A (p180), lymphocyte

function‐associated antigen 1; alpha polypeptide) 13.93

ITGBL1 integrin, beta‐like 1 (with EGF‐like repeat domains) 21.97

JAZF1 JAZF zinc finger 1 32.89

KAT6B K(lysine) acetyltransferase 6B 2.23

KATNAL1 katanin p60 subunit A‐like 1 2.63

KCNB1 potassium voltage‐gated channel, Shab‐related subfamily, member 1 131.34

KCNC1 potassium voltage‐gated channel, Shaw‐related subfamily, member 1 43.60


KCNQ5 potassium voltage‐gated channel, KQT‐like subfamily, member 5 11.18

KCTD12 potassium channel tetramerisation domain containing 12 2.29

KIAA1324 KIAA1324 7.80

KIAA1462 KIAA1462 9.85

KIAA1683 KIAA1683 2.34

KIF26B kinesin family member 26B 19.26




LEPR leptin receptor 15.92

LHCGR luteinizing hormone/choriogonadotropin receptor 14.78

LIMS2 LIM and senescent cell antigen‐like domains 2 47.15

LIPC lipase, hepatic 28.94

LIPN lipase, family member N 2.86

LOC10028703

6 hypothetical protein LOC100287036 6.17

LOC554223 hypothetical LOC554223 86.05

LOXL4 lysyl oxidase‐like 4 7.86



LY6D lymphocyte antigen 6 complex, locus D 28.96

MAF v‐maf musculoaponeurotic fibrosarcoma oncogene homolog (avian) 47.09

MAGI2 membrane associated guanylate kinase, WW and PDZ domain

containing 2 4.51

MAP7D2 MAP7 domain containing 2 10.41

MB myoglobin 3.06

MED12L mediator complex subunit 12‐like 4.51

MLIP muscular LMNA‐interacting protein 30.43

MRAP2 melanocortin 2 receptor accessory protein 2 7.37

MSI1 musashi homolog 1 (Drosophila) 67.82

MXD1 MAX dimerization protein 1 11.17

NEGR1 neuronal growth regulator 1 3.43

NOS3 nitric oxide synthase 3 (endothelial cell) 4.36

NOSTRIN nitric oxide synthase trafficker 25.09

NOVA2 neuro‐oncological ventral antigen 2 185.06

NPL N‐acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase) 11.92


NYNRIN KIAA1305 38.45

P2RX3 purinergic receptor P2X, ligand‐gated ion channel, 3 60.93

P4HA1 prolyl 4‐hydroxylase, alpha polypeptide I 8.17

PAPPA2 pappalysin 2 46.30

PARK2 Parkinson disease (autosomal recessive, juvenile) 2, parkin 9.27

PBX3 pre‐B‐cell leukemia homeobox 3 88.94

PCDHA9 protocadherin alpha 9 2.16

PDGFC platelet derived growth factor C 5.64

PDK3 pyruvate dehydrogenase kinase, isozyme 3 2.65

PIWIL4 piwi‐like 4 (Drosophila) 20.51

PKD1L1 polycystic kidney disease 1 like 1 14.95

PLAG1 pleiomorphic adenoma gene 1 18.21

PLAT plasminogen activator, tissue 5.04

PLXDC1 plexin domain containing 1 2.58

PLXNA4 plexin A4 39.31


interacting protein (liprin), alpha 1 2.03


PRELID2 PRELI domain containing 2 3.10

PRKAG2 protein kinase, AMP‐activated, gamma 2 non‐catalytic subunit 2.52

PRKAR2B protein kinase, cAMP‐dependent, regulatory, type II, beta 35.87

PRSS16 protease, serine, 16 (thymus) 2.11

PTAFR platelet‐activating factor receptor 11.49

PTPRC protein tyrosine phosphatase, receptor type, C 12.89

PTPRE protein tyrosine phosphatase, receptor type, E 2.37

PTPRR protein tyrosine phosphatase, receptor type, R 54.15

RAPGEF5 Rap guanine nucleotide exchange factor (GEF) 5 30.38


RASSF4 Ras association (RalGDS/AF‐6) domain family member 4 4.32

RDX radixin 2.01

RFESD Rieske (Fe‐S) domain containing 2.48

RFX3 regulatory factor X, 3 (influences HLA class II expression) 23.46

RGAG1 retrotransposon gag domain containing 1 3.24

RGMA RGM domain family, member A 18.12

RIN2 Ras and Rab interactor 2 11.91


ROS1 c‐ros oncogene 1 , receptor tyrosine kinase 2.11

RPS6KB1 ribosomal protein S6 kinase, 70kDa, polypeptide 1 2.21

RTDR1 rhabdoid tumor deletion region gene 1 39.71

SALL2 sal‐like 2 (Drosophila) 6.24

SCG5 secretogranin V (7B2 protein) 36.45

SCN2B sodium channel, voltage‐gated, type II, beta 8.43

SDC2 syndecan 2 6.96

SEMA5A

sema domain, seven thrombospondin repeats (type 1 and type 1‐like),

transmembrane domain (TM) and short cytoplasmic domain,

(semaphorin) 5A

2.44

SERPINE3 serpin peptidase inhibitor, clade E (nexin, plasminogen activator

inhibitor type 1), member 3 21.66

SFMBT2 Scm‐like with four mbt domains 2 9.62



SIAH3 seven in absentia homolog 3 (Drosophila) 35.56

SLC14A2 solute carrier family 14 (urea transporter), member 2 9.59

SLC22A11 solute carrier family 22 (organic anion/urate transporter), member 11 111.92

SLC2A14 solute carrier family 2 (facilitated glucose transporter), member 14 35.10

SLC2A5 solute carrier family 2 (facilitated glucose/fructose transporter),

member 5 2.06

SLC8A2 solute carrier family 8 (sodium/calcium exchanger), member 2 32.53

SOX2 SRY (sex determining region Y)‐box 2 3.74

SPTY2D1 SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae) 24.41

SWT1 Transcriptional protein SWT1 11.15


SYCP2L synaptonemal complex protein 2‐like 6.67

SYN2 synapsin II 2.64

TACR1 tachykinin receptor 1 51.44

TBX19 T‐box 19 2.14

TEK TEK tyrosine kinase, endothelial 25.59

TFEC transcription factor EC 8.70

TNFRSF13B tumor necrosis factor receptor superfamily, member 13B 547.26

TOX thymocyte selection‐associated high mobility group box 168.89

TRAF5 TNF receptor‐associated factor 5 3.54

TREM1 triggering receptor expressed on myeloid cells 1 466.94



TSHZ2 teashirt zinc finger homeobox 2 7.55


UBE2W ubiquitin‐conjugating enzyme E2W (putative) 7.36

UCHL1 ubiquitin carboxyl‐terminal esterase L1 (ubiquitin thiolesterase) 44.44

WTH3DI RAB6C‐like 3.40


ZDHHC22 zinc finger, DHHC‐type containing 22 41.79

ZFHX4 zinc finger homeobox 4 27.12




ZNF674 zinc finger family member 674 2.05

ZSCAN30 zinc finger and SCAN domain containing 30 2.19

Down‐regulated genes

ACSBG1 acyl‐CoA synthetase bubblegum family member 1 0.27


ADD3 adducin 3 (gamma) 0.26

ADRA1D adrenergic, alpha‐1D‐, receptor 0.01

AMACR C1q and tumor necrosis factor related protein 3; alpha‐methylacyl‐CoA

racemase 0.07

AMMECR1 Alport syndrome, mental retardation, midface hypoplasia and

elliptocytosis chromosomal region gene 1 0.11




ARRB1 arrestin, beta 1 0.36

ASB14 ankyrin repeat and SOCS box‐containing 14 0.10

ATP8B4 ATPase, class I, type 8B, member 4 0.09


BCMO1 beta‐carotene 15,15'‐monooxygenase 1 0.01

BST1 bone marrow stromal cell antigen 1 0.05

BTBD16 BTB (POZ) domain containing 16 0.05

BTC betacellulin 0.03







CAPZB capping protein (actin filament) muscle Z‐line, beta 0.47

CCL17 chemokine (C‐C motif) ligand 17 0.00


CDH22 cadherin‐like 22 0.08

CFI complement factor I 0.32

CFP complement factor properdin 0.03

CGREF1 cell growth regulator with EF‐hand domain 1 0.46

CHRNB2 cholinergic receptor, nicotinic, beta 2 (neuronal) 0.42

CTRC chymotrypsin C (caldecrin) 0.02


DCLK1 doublecortin‐like kinase 1 0.36

DNAH3 dynein, axonemal, heavy chain 3 0.12

DPT dermatopontin 0.04

DPYSL5 dihydropyrimidinase‐like 5 0.05

DTX3L deltex 3‐like (Drosophila) 0.39

EFCAB5 EF‐hand calcium binding domain 5 0.04

EFTUD2 elongation factor Tu GTP binding domain containing 2 0.45

EIF2AK2 eukaryotic translation initiation factor 2‐alpha kinase 2 0.43

EIF4A1 eukaryotic translation initiation factor 4A, isoform 1 0.35

ELAC2 elaC homolog 2 (E. coli) 0.38

EPB41L3 erythrocyte membrane protein band 4.1‐like 3 0.05

EPHA4 EPH receptor A4 0.06

ERAP2 endoplasmic reticulum aminopeptidase 2 0.08




FCER1G Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide 0.31

FIGF c‐fos induced growth factor (vascular endothelial growth factor D) 0.03



GABRR2 gamma‐aminobutyric acid (GABA) receptor, rho 2 0.03

GBP5 guanylate binding protein 5 0.07

GCNT7 glucosaminyl (N‐acetyl) transferase family member 7 0.37

GFAP glial fibrillary acidic protein 0.09

GFOD1 glucose‐fructose oxidoreductase domain containing 1 0.50

GIPC2 GIPC PDZ domain containing family, member 2 0.38

GLRB glycine receptor, beta 0.09

GMPR guanosine monophosphate reductase 0.14

GPR37 G protein‐coupled receptor 37 (endothelin receptor type B‐like) 0.04


GRAP2 GRB2‐related adaptor protein 2 0.16

HIST1H2BL histone cluster 1, H2bl 0.17

HIST4H4

histone cluster 1, H4l; histone cluster 1, H4k; histone cluster 4, H4;

histone cluster 1, H4h; histone cluster 1, H4j; histone cluster 1, H4i;

histone cluster 1, H4d; histone cluster 1, H4c; histone cluster 1, H4f;

histone cluster 1, H4e; histone cluster 1, H4b; histone cluster 1, H4a;

histone cluster 2, H4a; histone cluster 2, H4b 0.38

HMP19 HMP19 protein 0.08



HPGD hydroxyprostaglandin dehydrogenase 15‐(NAD) 0.20

HRASLS2 HRAS‐like suppressor 2 0.02

IFIH1 interferon induced with helicase C domain 1 0.33




IL34 interleukin 34 0.50

ITIH5 inter‐alpha (globulin) inhibitor H5 0.08

ITK IL2‐inducible T‐cell kinase 0.02


KCNRG potassium channel regulator 0.05

KIAA0232 KIAA0232 0.44

KIAA1107 KIAA1107 0.41

KLRC4 killer cell lectin‐like receptor subfamily C, member 4 0.03

KLRC4‐KLRK1 KLRC4‐KLRK1 Read‐Through Transcript 0.04

LAMP3 lysosomal‐associated membrane protein 3 0.30

LCLAT1 lysocardiolipin acyltransferase 1 0.45

LDB3 LIM domain binding 3 0.10


LRP1B low density lipoprotein‐related protein 1B (deleted in tumors) 0.09

MAK male germ cell‐associated kinase 0.12

MARK2 MAP/microtubule affinity‐regulating kinase 2 0.49

MMRN1 multimerin 1 0.03

MYBPHL myosin binding protein H‐like 0.01

MYO9B myosin IXB 0.34

NIPAL2 NIPA‐like domain containing 2 0.20

NME5 non‐metastatic cells 5, protein expressed in (nucleoside‐diphosphate

kinase) 0.01

NR0B2 nuclear receptor subfamily 0, group B, member 2 0.01

NR1D2 nuclear receptor subfamily 1, group D, member 2 0.08


NT5C1B‐RDH1

4 NT5C1B‐RDH14 Read‐Through Transcript

0.09

OTX1 orthodenticle homeobox 1 0.43

PABPC4L poly(A) binding protein, cytoplasmic 4‐like 0.00

PADI4 peptidyl arginine deiminase, type IV 0.02

PARD3B par‐3 partitioning defective 3 homolog B (C. elegans) 0.09






PGPEP1L pyroglutamyl‐peptidase 1‐like 0.04

PIK3AP1 phosphoinositide‐3‐kinase adaptor protein 1 0.39

PLVAP plasmalemma vesicle associated protein 0.03

PMF1‐BGLAP PMF1‐BGLAP Read‐Through Transcript 0.46

POC1B‐GALN

T4 POC1B‐GALNT4 Read‐Through Transcript

0.12

POF1B premature ovarian failure, 1B 0.02

PPARD peroxisome proliferator‐activated receptor delta 0.41

PPP6C protein phosphatase 6, catalytic subunit 0.50

PRICKLE1 prickle homolog 1 (Drosophila) 0.06

PRPH2 peripherin 2 (retinal degeneration, slow) 0.02

PRR5‐ARHGA

P8

Rho GTPase activating protein 8; proline rich 5 (renal); PRR5‐ARHGAP8

fusion 0.05

PSMD1 proteasome (prosome, macropain) 26S subunit, non‐ATPase, 1 0.06

PTPRB protein tyrosine phosphatase, receptor type, B 0.13

RAB9B RAB9B, member RAS oncogene family 0.02


RAP1GDS1 RAP1, GTP‐GDP dissociation stimulator 1 0.50


RBP1 retinol binding protein 1, cellular 0.36


SAMD5 sterile alpha motif domain containing 5 0.13

SAMHD1 SAM domain and HD domain 1 0.33

SDHD

similar to succinate dehydrogenase complex, subunit D, integral

membrane protein; succinate dehydrogenase complex, subunit D,

integral membrane protein 0.06

SECTM1 secreted and transmembrane 1 0.43

SEMA6A sema domain, transmembrane domain (TM), and cytoplasmic domain,

(semaphorin) 6A 0.49

SGPP2 sphingosine‐1‐phosphate phosphotase 2 0.03

SIDT1 SID1 transmembrane family, member 1 0.01

SLC25A13 solute carrier family 25, member 13 (citrin) 0.30

SLC7A7 solute carrier family 7 (cationic amino acid transporter, y+ system), 0.09

member 7


member 8 0.08

SLFN11 schlafen family member 11 0.25

SRL sarcalumenin 0.48

ST18 suppression of tumorigenicity 18 (breast carcinoma) (zinc finger

protein) 0.01



STOX1 storkhead box 1 0.48

STX19 syntaxin 19 0.06

STXBP5L syntaxin binding protein 5‐like 0.17

SYNJ2BP‐COX

16 SYNJ2BP‐COX16 Read‐Through Transcript

0.04

SYNPO2 synaptopodin 2 0.45


TBRG4 transforming growth factor beta regulator 4 0.46

TEX19 testis expressed 19 0.48


TMC6 transmembrane channel‐like 6 0.47

TMEM232 hypothetical protein LOC642987 0.47


TMPRSS6 transmembrane protease, serine 6 0.31

TNFRSF8 tumor necrosis factor receptor superfamily, member 8 0.05

TNFSF10 tumor necrosis factor (ligand) superfamily, member 10 0.47

TOMM40 translocase of outer mitochondrial membrane 40 homolog (yeast) 0.41

TRANK1 lupus brain antigen 1 0.24




TTC23L tetratricopeptide repeat domain 23‐like 0.01

ULK2 unc‐51‐like kinase 2 (C. elegans) 0.29



WNT2B wingless‐type MMTV integration site family, member 2B 0.03

XYLT1 xylosyltransferase I 0.11

YTHDF2 YTH domain family, member 2 0.47

ZFAT zinc finger and AT hook domain containing 0.44

ZKSCAN5 zinc finger with KRAB and SCAN domains 5 0.45


Supplementary Table 9. Primers sequences

Name Sequence

Primers for constructing down-regulated miRNAs in Hep-12 cells

miR-122： PF: 5'CGGGATCCACAGGAAGTTTTTGCAGAAG

PR: 5'CCGCTCGAGAGCATGTGAGAGGCAGGGTTC

miR-126: PF: 5'CGGGATCCTATGCCGCCTAAGTACGTC

PR: 5'CCGCTCGAGAGCCTCATATCAGCCAAGAAG

miR-130a PF: 5'CGGGATCCAGGGGGTTGGTGAAGAAGG

PR: 5'CCGCTCGAGTTTCACAGTAACGGAGGCAG

miR-149 PF: 5'CGGGATCCTCCTGCCTTTGACTGCCG

PR: 5'CCGCTCGAGTCAGCCACCTCTCACACC

miR-182 PF: 5'CGGAATTCTGCAGGTTACAGATATGAGG

PF: 5'CGGGATCCTGCAGGTTACAGATATGAG

miR-183 PF: 5'CGGGATCCTGGGGCATGTGGATCTTGTG

PR: 5'CCGCTCGAGTCCTGCTTTTCCCATATTG

miR-200b PF: 5'CGGGATCCTCAGACAAGGCAGCACGTG

PR: 5'CCGCTCGAGTTGCATTCCGGGGTCTCTG

miR-221 PF: 5'CGGGATCCAGTTTATCTATCCGACCTTC

PR: 5'CCGCTCGAGACTAGGCTGGTGTGTGAGAC

miR-222 PF: 5'CGGGATCCAGGAATCATGTATGCTGTAG

PR: 5'CCGCTCGAGACTTAACACCCTAGAACTTG

miR-224 PF: 5'CGGGATCCTACTACCTTTGACTTGGGAG

PR: 5'CCGCTCGAGAAGAGTTTGAGACCAGTCC

miR-23a PF: 5'CGGGATCCAAGCATCTGGGGACCTGGAG

PR: 5'CCGCTCGAGACTTAGCCACTGTGAACACG

miR-23b PF: 5'CGGGATCCTCATCTCTGGAGTCCCTTTG

PR: 5'CCGCTCGAGTTGTTAGAGAGGTCATCGCTG

miR-28 PF: 5'CGGGATCCAGAAGTGTCCTGAATGTTTAC

PR: 5'CCGCTCGAGTGACAAAGAGGAGCTAGAAG

miR-29a PF: 5'CGGGATCCTTGTACAGGATATCGCATTG

PR: 5'CCGCTCGAGTCAACTTAGAAACTGGAAGA

miR-31 PF: 5'CGGGATCCACCTCCTGTGCCTAACTAC

PR: 5'CCGCTCGAGAGGTGTGTCCAAGGAATAG

miR-424 PF: 5'CGGGATCCTCGCTCTGCTTTTCACCCAC

PR: 5'CCGCTCGAGAATACTGCCCTCCCCGGAC

miR-452 PF: 5'CGGGATCCTCACATTCCTTTCCAGTTTC

PR: 5'CCGCTCGAGACTGGATTGGTTCTGGGTATG

miR-455

PF: 5'CGGGATCCAGCCGCTGTTAGTTAATGCC

PR: 5'CCGCTCGAGAATGTAGCCCTAGGAAAGAG

miR-663 PF: 5'CGGAATTCTGGACGAGAATCACGAGCG

PR: 5'CCGCTCGAGACCAACCGACGTAAAGCC

miR-99b PF: 5'CGGGATCCAGGCTTTGGATCTGGACTC

PR: 5'CCGCTCGAGACAGACCCGACAGACAGAC

Let-7a PF: 5'CGGGATCCAAGAAGCAAAAGGTTTCCCC

PR: 5'CCGCTCGAGAGCGGATTCAGATAACCAAG

miR-21 PF: 5'CGGGATCCGATTGAACTTGTTCATTTTG

PR: 5'CCGCTCGAGAAGACTATCCCCATTTCTCCA

miR-34a PF: 5'CGGATCCCGGGCTGGAGAGAC

PR: 5'CCGCTCGAGCCTGTGCCTTTTTCCTTCC

Let-7b PF: 5’CGGGATCCATTGAATCTAGCTCCCAGATGC

PR: 5’CCGCTCGAGCAGGAAGTGAGAGGAACAGC

Let-7d PF: 5’CGGGATCCAGGAGGAACAGCTGAGAGTC

PR: 5’CCGCTCGAGTCGTTTGTGACTTGAGGTTG

Let-7e PF: 5’CGGGATCCAGGAGGGGATGCAGGGACAAG

PR: 5’CCGCTCGAGACCCGTAGAACCGACCTTGC

Let-7f PF: 5’CGGGATCCAGTGCAGCATTTGTTTATGG

PR: 5’ CCGCTCGAGCTATGAAGATTTCCTGAAGG

Let-7g PF: 5’CGGGATCCACTGGTTTATTTCTTCTGTTG

PR: 5’CCGCTCGAGAGTCATCCCAGGGGTTCACAG

Let-7c PF: 5’CACGGATCGACATTTTACGTGACCTATC

PR: 5’CACCTCGAGCATGGAGTGACAACCCATTAG

miR-125a PF: 5’CGGGATCCAGTAGGTTGTGAAGCAGAGG

PR: 5’CCGCTCGAGTCTGACTCCCTCTTATTCTG

Primers for constructing up-regulated miRNAs in Hep-12 cells

miR-10b PF:5'CGGGATCC AGTACCCCAAAACCTAGCC

PR:5'CCGCTCGAG TGTCGCCAAGCCCATTAGG

miR-1224

PF:5'CGGGATCC TGATGATCCCCACTGCAGG

PR:5'CCGCTCGAG ACTGTCACCCTGGCCAAC

miR-124-1

PF:5'CGGGATCC ATGGGGGAGAACAAAGAGC

PR:5'CCGCTCGAG TGCATCTCTAAGCCCCTGTC

miR-124-2

PF:5'CGGGATCC AACAGACTAATTAACAGCGG

PR:5'CCGCTCGAG TTATGCGGCAAGAGATGGG

miR-124-3

PF:5'CGGGATCC AAAGGGGAGAAGTGTGGGC

PR:5'CCGCTCGAG CATTGTTCGCCGGATTTGTC

miR-125b-1

PF:5'CGGGATCC ACCATACCACCTGTTTGTTG

PR:5'CCGCTCGAG TATACTCAATCACCTCAGAC

miR-125b-2

PF:5'CGGGATCC ATGGTCGTCGTGATTACTC

PR:5'CCGCTCGAG AGCATTGTTCTTTTCTCCTAG

miR-130b

PF:5'CGGGATCC ATGATTCTCCAGCTCTGCAC

PR:5'CCGCTCGAG AATTCGCTCCCTTCTCCATG

miR-132

PF:5'CGGGATCC ACAGTCTCCAGTCACGGCC

PR:5'CCGCTCGAG ACGTGGGATCTTGACTCGC

miR-137

PF:5'CGGGATCC TTTATGGTCCCGGTCAAGC

PR:5'CCGCTCGAG AACCCATTTTCCAGTCCTG

miR-148a

PF:5'CGGGATCC TTCCATTATCGGTCGCATCC

PR:5'CCGCTCGAG ATTGGTCAAGTTCCTCGTGC

miR-148b PF:5'CGGGATCC AGGACAATGGACTAGGCTT

PR:5'CCGCTCGAG TCTGTCTAAGTCACCCAATC

miR-192 PF:5'CGGGATCC AGTGGGGCTGCTGTTATCT

PR:5'CCGCTCGAG TCTGCTGACTGCTGGACAC

miR-194-2

PF:5'CGGGATCC ATGATAAGAAGCCTCGGTG

PR:5'CCGCTCGAG AATTCATAGGTCAGAGCCC

miR-204

PF:5'CGGGATCC TGATGGAAAGGAGGGTGGG

PR:5'CCGCTCGAG TTATGGGACAGTTATGGGCC

miR-216a

PF:5'CGGGATCC TGTGAATTCAGCAAGAGGAG

PR:5'CCGCTCGAG TCCTTTCCAGCACAACAGC

miR-217

PF:5'CGGGATCC ATCTCTCTTGGTAAATTGGG

PR:5'CCGCTCGAG AGAACGGTGGTAAATGATAG

miR-375 PF:5'CGGGATCC AGTATAAGAGCACACGGAGC

PR:5'CCGCTCGAG TTACGACGCAGAATGGAGC

miR-483 PF:5'CGGGATCC ATTTGGGGGTAGGAAGTGG

PR:5'CCGCTCGAG AAATGTGTGGGATGTGAGC

miR-512-1

PF:5'CGGGATCC TGTTATTCAGGCTGGGGAC

PR:5'CCGCTCGAG TTAGCTTTTACCTGCAGTGG

miR-512-2

PF:5'CGGGATCC AGCAACATTCAGAAGTCAG

PR:5'CCGCTCGAG TTTATGGCGCAGAACAAGC

miR-515

PF:5'CGGGATCC AGTAGAGACGGAGTTTCAC

PR:5'CCGCTCGAG ACAGAACCCCAACATCATG

miR-516a

PF:5'CGGGATCC CTAACCTGCTGATTCTTTGA

PR:5'CCGCTCGAG TGTATTACCAAGATCAGCGT

miR-516b-1

PF:5'CGGGATCC TCCAGGAAACATGCAAACAG

PR:5'CCGCTCGAG AGATCTAGGTTGGAAGTGC

miR-517a PF:5'CGGGATCC TGAACCCAGGAGGCAGAAG

PR:5'CCGCTCGAG CTGATGATAAGCACGCTCTG

miR-517b

PF:5'CGGGATCCAGGCTAAGGCTTGAGAATG

PR:5'CCGCTCGAGAGCCCAAGAGATCTCGGTT

miR-517c

PF:5'CGGGATCCAGAAGGAGATTGCAGTGAG

PR:5'CCGCTCGAGAACCCCAACATCATGCACG

miR-518b

PF:5'CGGGATCCACCTGCTGAGCCTTTGAAG

PR:5'CCGCTCGAGAGCCCAAGAGATCTAGGTAG

miR-518d:

PF:5'CGGGATCCGAAGCAAAGAACCAGAGATG

PR:5'CCGCTCGAGAAGAGACCTAGGTTGGAAG

miR-518e PF:5'CGGGATCCAGTGGTTTATGTTCTGGATTC

PR:5'CCGCTCGAGTGAACCCAAGAGATCTAGG

miR-518f PF:5'CGGGATCCACCTGCTGATCCTTTGAAG

PR:5'CCGCTCGAGAACACCAACATCATCCACG

miR-519a-1 PF:5'CGGGATCCTTGAGGGAAGGAACTGGAG

PR:5'CCGCTCGAGTCAGAAGCCCAACATCATC

miR-519a-2 PF:5'CGGGATCCAGAAATCCAGCCTAATCCTC

PR:5'CCGCTCGAGTGAGCCCAAGAGATCTAGG

miR-519c PF 5'CGGGATCCAACAAGGAACTGGAGATGG

PR:5'CCGCTCGAGAAGAGAGCTAGGTTGGAAG

miR-519d PF:5'CGGGATCCACCTGCAGAGCCTTTGAAG

PR:5'CCGCTCGAGACTCCCAACATCATCCAAG

miR-519e PF 5'CGGGATCCAAGCAAGGAACTGGAGATG

PR:5'CCGCTCGAGATGCGTTACCAAGATCAGC

miR-520a PF:5'CGGGATCCAAGAAGGAACTGGAGATGG

PR:5'CCGCTCGAGAGAACCCCAACATCATCCG

miR-520c PF:5'CGGGATCCGAAGGAACTGGAGATGGTC

PR:5'CCGCTCGAGAGAACCCCAACATCATCCG

miR-520g

PF:5'CGGGATCCTGTAAGGTATGAGTAGTAGG

PR:5'CCGCTCGAGAACCCCAACATCATCCAAG

miR-520h PF:5'CGGGATCCACCTGCTGAGCCTTTGAAG

PR:5'CCGCTCGAGAACCCCAACATCATCCAAG

miR-522 PF:5'CGGGATCCAAGCAAGGAACTGGAGATG

PR:5'CCGCTCGAGAAGAGGTCTAGGTTGGAAG

miR-525 PF:5'CGGGATCCAAGGAACTGGAGATGGTCG

PR:5'CCGCTCGAGACCCACCATCATCCAAGTC

miR-629 PF:5'CGGGATCCAATCCCTGCTTCCACTTTG

PR:5'CCGCTCGAGAACAATGCCACACAGATGC

miR-7-1 PF:5'CGGGATCCAACTTCTCATTTCTCTGGTG

PR:5'CCGCTCGAGATCGGACATTAGTAGAACAG

miR-7-2 PF:5'CGGGATCCTCTGCCGATGGGTGTTTAG

PR:5'CCGCTCGAGATGAACTTAGTAATAGGAGCG

miR-7-3 PF:5'CGGGATCCACGAGTGATGTGACAAACC

PR:5'CCGCTCGAGAACCGGGAATGGAAAACAG

miR-708 PF:5'CGGGATCCACTGGTGACTTCATTCCCC

PR:5'CCGCTCGAGTTGAGTTGGCAGTGCTGTG

miR-886 PF:5'CGGGATCCAGGACACGTTAGCAGGAC

PR:5'CCGCTCGAGATACTTTCTGTCACACCTTC

miR-9-2 PF:5'CGGGATCCACACACAAACAGAAACCAGG

PR:5'CCGCTCGAGTGCAACAACCCCTCTCAAG

miR-95 PF:5'CGGGATCCACCAGTTCCATTTGCACAC

PR:5'CCGCTCGAGACGCTTCTCCAGGTCAGG

miR-99a PF:5'CGGGATCCTGCATCCTTAGAACTCAGC

PR:5'CCGCTCGAGTCGAACTTGAATGGGTGTG

PolyA tailing qRT-PCR primers

OligodT adapter 5'GCGAGCACAGAATTAATACGACTCACTATAGGTTTTT

TTTTTTTVN

Reverse primer 5' GCGAGCACAGAATTAATACGAC

Let-7c forward 5' GTTGAGGTAGTAGGTTGTATGGTT

miR-200b forward 5’TAATACTGCCTGGTAATGATGAC

miR-222 forward 5'AGCTACATCTGGCTACTGGGT

miR-424 forward 5'GCAGCAGCAATTCATGTTTTGAA

Primers for construction of PBX3 3’UTR and corresponding mutation

PBX3- 3’UTR-PF 5' TGCTCTAGAccggTCTCTGGCCACACTTTTCCCTG

PBX3- 3’UTR-PR 5’CGGAATTCATGCATACATATAACTACCACGAGGAAG

AC

PBX3-200b-mut-PR 5’GACGTCAAAATCTGGACACATCACAATTAGTCGCTG

CTT

PBX3-200b-mut-PF

5’TGTCCAGATTTTGACGTCCAGTACTGTATATTTCACCC

TG

PBX3-222-mut-PF 5’AAGACGAAATTTCAATGTATTCCGCGATCTAGAGTGC

TCACTTACTACCTC

PBX3-222-mut- PR： 5’GATCGCGGAATACATTGAAATTTCGTCTTTTTGTATG

AGTTCGCATGAGG

PBX3-424-mut2-PF 5’AGACGAAGATACTGTAGTAGTATAGAGGTGAAAACG

AGATTG

PBX3-424-mut2-PR 5’ACTACTACAGTATCTTCGTCTCTCAGAACAATC

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