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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.

From: Apert p.Ser252Trp Mutation in FGFR2 Alters Osteogenic Potential and Gene Expression of Cranial Periosteal Cells

Gene (Official Symbol) Gene name Accession number P value Apert-to-control Ratio (Log2) x-fold up-or down-regulated in Apert
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
  1. aGenes within the list of 120 genes identified as differentially expressed in at least 50 percent of the “leave-one-out” datasets.
  2. bThose within the list of 25 genes identified as differentially expressed in 100 percent of the “leave-one-out” datasets (see Methods for details).