Table 3 98 genes grouped in functional categories. Transcripts are ordered by their Apert-to-control ratios (Log 2). Upregulated genes in AS cells are shown in orange. Downregulated genes are shown in blue.

Positive regulation of cell proliferation

CIP29

cytokine induced protein 29 kDa

NM_033082.1

0.040

1.24

2.36

TCF19

transcription factor 19 (SC1)

BC033086.1

0.041

1.23

2.34

SPBC25 ^b

spindle pole body component 25 homolog (S. cerevisiae)

NM_020675.3

0.010

1.18

2.27

STMN1 ^b

stathmin 1/oncoprotein 18

NM_203401.1

0.006

1.11

2.16

SPAG5 ^b

sperm associated antigen 5

NM_006461.2

0.007

0.98

1.97

MCM4

MCM4 minichromosome maintenance deficient 4 (S. cerevisiae)

NM_182746.1

0.030

0.90

1.87

HCAP-G

chromosome condensation protein G

NM_022346.2

0.028

0.87

1.83

RRM2 ^b

ribonucleotide reductase M2 polypeptide

NM_001034.1

0.019

0.86

1.81

AURKB

aurora kinase B

NM_004217.1

0.031

0.84

1.79

NEK6 ^b

NIMA (never in mitosis gene a)-related kinase 6

NM_014397.3

0.017

0.74

1.67

CKAP2

cytoskeleton associated protein 2

NM_018204.2

0.037

0.66

1.58

NEDD1

neural precursor cell expressed, developmentally downregulated 1

NM_152905.2

0.041

0.62

1.53

RNASEH2A ^b

ribonuclease H2, subunit A

NM_006397.2

0.011

0.60

1.52

UFD1L ^b

ubiquitin fusion degradation 1 like (yeast)

NM_005659.3

0.023

0.59

1.51

PLK3

polo-like kinase 3 (Drosophila)

NM_004073.2

0.036

0.57

1.48

CKLF ^b

chemokine-like factor

NM_016951.2

0.021

0.55

1.46

TK1

thymidine kinase 1, soluble

NM_003258.1

0.028

0.50

1.41

DTYMK

deoxythymidylate kinase

NM_012145.2

0.037

0.44

1.36

MUS81 ^b

MUS81 endonuclease homolog (S. cerevisiae)

NM_025128.3

0.024

0.44

1.35

MAPRE1

microtubule-associated protein, RP/EB family, member 1

NM_012325.1

0.045

0.38

1.30

HECA ^b

headcase homolog (Drosophila)

NM_016217.1

0.047

−0.62

1.54

CSNK2A1

casein kinase 2, α 1 polypeptide

NM_177560.2

0.030

−0.73

1.66

BCL6 ^a

B-cell CLL/lymphoma 6 (zinc finger protein 51)

NM_001706.2

0.013

−0.74

1.67

BCL3

B-cell CLL/lymphoma 3

NM_005178.2

0.039

−0.79

1.73

ADAM33

ADAM metallopeptidase domain 33

NM_153202.1

0.027

−1.22

2.33

PDGFRA

platelet-derived growth factor receptor, α polypeptide

NM_006206.2

0.045

−1.34

2.53

ChGn ^a

chondroitin beta1,4 N-acetylgalactosaminyltransferase

NM_018371.3

0.015

−1.42

2.68

PIK3C2B ^a

phosphoinositide-3-kinase, class 2, β polypeptide

NM_002646.2

0.004

−1.54

2.91

Negative regulation of cell proliferation

RAD1 ^b

RAD1 homolog (S. pombe)

NM_002853.2

0.018

0.73

1.66

CDKN3

cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase)

NM_005192.2

0.044

0.60

1.52

RBM5 ^b

RNA binding motif protein 5

NM_005778.1

0.024

−0.69

1.61

ING4

inhibitor of growth family, member 4

NM_198287.1

0.044

−0.69

1.62

IFITM3

interferon induced transmembrane protein 3 (1-8U)

NM_021034.1

0.033

−0.83

1.77

KLF11

Kruppel-like factor 11

NM_003597.4

0.039

−0.92

1.89

MTSS1 ^b

metastasis suppressor 1

NM_014751.2

0.009

−1.14

2.20

RARRES3 ^b

retinoic acid receptor responder (tazarotene induced) 3

NM_004585.2

0.022

−1.64

3.12

Nucleotide metabolism

CTPS

CTP synthase

NM_001905.1

0.046

0.98

1.98

RRM2 ^b

ribonucleotide reductase M2 polypeptide

NM_001034.1

0.019

0.86

1.81

PRPS1L1 ^b

phosphoribosyl pyrophosphate synthetase 1-like 1

NM_175886.2

0.022

0.71

1.63

POLR3K ^b

polymerase (RNA) III (DNA directed) polypeptide K

NM_016310.2

0.013

0.69

1.61

RRM1

ribonucleotide reductase M1 polypeptide

NM_001033.2

0.045

0.55

1.46

TK1

thymidine kinase 1, soluble

NM_003258.1

0.028

0.50

1.41

DTYMK

deoxythymidylate kinase

NM_012145.2

0.037

0.44

1.36

ADCY2 ^b

adenylate cyclase 2 (brain)

NM_020546.1

0.028

0.41

1.33

ATP5G1

ATP synthase, H + transporting, mitochondrial F0 complex, subunit C1 (subunit 9)

NM_005175.1

0.042

0.28

1.22

PDE6G ^b

phosphodiesterase 6G, cGMP-specific, rod, gamma

NM_002602.1

0.003

−0.53

1.44

Regulation of gene expression

CIP29

cytokine induced protein 29 kDa

NM_033082.1

0.040

1.24

2.36

ZNF738 ^a

zinc finger protein 738

BC034499.1

0.003

1.03

2.04

POLR3K ^b

polymerase (RNA) III (DNA directed) polypeptide K

NM_016310.2

0.013

0.69

1.61

ELAVL1

ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)

NM_001419.2

0.041

0.67

1.59

HIP2 ^b

huntingtin interacting protein 2

NM_005339.3

0.017

0.58

1.49

CREB3 ^b

cAMP responsive element binding protein 3

NM_006368.4

0.023

0.46

1.38

CASP8AP2

CASP8 associated protein 2

NM_012115.2

0.049

0.41

1.33

ZNF414 ^b

zinc finger protein 414

NM_032370.1

0.029

0.41

1.32

GABPB2

GA binding protein transcription factor, β subunit 2

NM_002041.2

0.027

0.40

1.32

SMARCA4

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4

NM_003072.2

0.034

0.39

1.31

SIX5 ^b

sine oculis homeobox homolog 5 (Drosophila)

NM_175875.3

0.017

−0.49

1.40

ZNF44

zinc finger protein 44

BC032246.1

0.032

−0.57

1.49

ZFHX4

zinc finger homeodomain 4

NM_024721.2

0.030

−0.58

1.49

MITF

microphthalmia-associated transcription factor

NM_006722.1

0.042

−0.60

1.51

ZNF688

zinc finger protein 688

NM_145271.2

0.026

−0.61

1.53

TNIP2 ^b

TNFAIP3 interacting protein 2

NM_024309.2

0.008

−0.62

1.54

ING4

inhibitor of growth family, member 4

NM_198287.1

0.044

−0.69

1.62

BCL6 ^a

B-cell CLL/lymphoma 6 (zinc finger protein 51)

NM_001706.2

0.013

−0.74

1.67

ELL3 ^b

elongation factor RNA polymerase II-like 3

NM_025165.1

0.006

−0.74

1.67

PPARA ^b

peroxisome proliferative activated receptor, α

NM_032644.1

0.009

−0.74

1.67

RELB

v-rel reticuloendotheliosis viral oncogene homolog B, nuclear factor of kappa light polypeptide gene enhancer in B-cells 3 (avian)

NM_006509.2

0.033

−0.74

1.67

ZFP64 ^b

zinc finger protein 64 homolog (mouse)

NM_018197.2

0.017

−0.78

1.72

BCL3

B-cell CLL/lymphoma 3

NM_005178.2

0.039

−0.79

1.73

NFIL3 ^b

nuclear factor, interleukin 3 regulated

NM_005384.1

0.012

−0.83

1.77

ANKZF1

ankyrin repeat and zinc finger domain containing 1

NM_018089.1

0.036

−0.85

1.81

ARID5A

AT rich interactive domain 5A (MRF1-like)

NM_006673.2

0.042

−0.92

1.89

KLF11

Kruppel-like factor 11

NM_003597.4

0.039

−0.92

1.89

CREB5 ^b

cAMP responsive element binding protein 5

NM_004904.1

0.010

−1.00

2.00

PNRC1 ^a

proline-rich nuclear receptor coactivator 1

NM_006813.1

0.008

−1.05

2.07

ATF3

activating transcription factor 3

NM_004024.2

0.049

−1.10

2.14

MAF

v-maf musculoaponeurotic fibrosarcoma oncogene homolog (avian)

NM_005360.2

0.044

−1.19

2.29

ZNF385 ^b

zinc finger protein 385

NM_015481.1

0.011

−1.38

2.61

Cell Adhesion

HAPLN1 ^a

hyaluronan and proteoglycan link protein 1

NM_001884.2

0.005

3.00

7.99

CIB1 ^b

calcium and integrin binding 1 (calmyrin)

NM_006384.2

0.035

0.32

1.25

FLRT2

fibronectin leucine rich transmembrane protein 2

NM_013231.3

0.042

−0.64

1.56

CNTNAP1

contactin associated protein 1

NM_003632.1

0.041

−0.72

1.64

CSNK2A1

casein kinase 2, α 1 polypeptide

NM_177560.2

0.030

−0.73

1.66

LGALS3BP ^b

lectin, galactoside-binding, soluble, 3 binding protein

NM_005567.2

0.014

−0.89

1.85

PERP

PERP, TP53 apoptosis effector

NM_022121.2

0.042

−0.92

1.89

ADAM8 ^b

a disintegrin and metalloproteinase domain 8

NM_001109.1

0.044

−1.06

2.08

CLDN15 ^b

claudin 15

NM_014343.1

0.022

−1.13

2.19

ADAM33

ADAM metallopeptidase domain 33

NM_153202.1

0.027

−1.22

2.33

PDGFRA

platelet-derived growth factor receptor, α polypeptide

NM_006206.2

0.045

−1.34

2.53

TNXB ^b

tenascin XB

NM_032470.2

0.015

−2.32

4.98

DKFZp434 B1231 ^b

eEF1A2 binding protein

NM_178275.3

0.010

−2.66

6.31

Extracellular matrix component, biosynthesis

HAPLN1 ^a

hyaluronan and proteoglycan link protein 1

NM_001884.2

0.005

3.00

7.99

TIMP3 ^a

TIMP metallopeptidase inhibitor 3

BG104808.1

0.006

0.42

1.34

BMP1 ^b

bone morphogenetic protein 1

NM_006129.2

0.024

−0.62

1.54

B4GALT7 ^b

xylosylprotein β 1,4-galactosyltransferase, polypeptide 7 (galactosyltransferase I)

NM_007255.1

0.026

−0.66

1.57

MATN2

matrilin 2

NM_030583.1

0.027

−0.96

1.95

ChGn ^a

chondroitin beta1,4 N-acetylgalactosaminyltransferase

NM_018371.3

0.015

−1.42

2.68

TNXB ^b

tenascin XB

NM_032470.2

0.015

−2.32

4.98

MAPK signaling pathway

DUSP2 ^b

dual specificity phosphatase 2

NM_004418.2

0.004

1.17

2.25

STMN1 ^b

stathmin 1/oncoprotein 18

NM_203401.1

0.006

1.11

2.16

PLA2G12A

phospholipase A2, group XIIA

NM_030821.3

0.044

0.39

1.31

PDE6G ^b

phosphodiesterase 6G, cGMP-specific, rod, gamma

NM_002602.1

0.003

−0.53

1.44

TNIP2 ^b

TNFAIP3 interacting protein 2

NM_024309.2

0.008

−0.62

1.54

UCN

urocortin

NM_003353.2

0.044

−0.65

1.57

CASP7 ^b

caspase 7, apoptosis-related cysteine peptidase

NM_001227.2

0.023

−0.65

1.57

MAP3K6

mitogen-activated protein kinase kinase kinase 6

NM_004672.3

0.041

−0.67

1.59

BCL3

B-cell CLL/lymphoma 3

NM_005178.2

0.039

−0.79

1.73

MAPK8IP1

mitogen-activated protein kinase 8 interacting protein 1

NM_005456.2

0.037

−0.86

1.81

SPTBN1

spectrin, beta, non-erythrocytic 1 (SPTBN1)

NM_003128.1

0.049

−0.87

1.83

KLF11

Kruppel-like factor 11

NM_003597.4

0.039

−0.92

1.89

PNRC1 ^a

proline-rich nuclear receptor coactivator 1

NM_006813.1

0.008

−1.05

2.07

PDGFRA

platelet-derived growth factor receptor, α polypeptide

NM_006206.2

0.045

−1.34

2.53

PIK3C2B ^a

phosphoinositide-3-kinase, class 2, β polypeptide

NM_002646.2

0.004

−1.54

2.91

RARRES3 ^b

retinoic acid receptor responder (tazarotene induced) 3

NM_004585.2

0.022

−1.64

3.12