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. Author manuscript; available in PMC: 2012 Aug 1.
Published in final edited form as: Melanoma Res. 2011 Aug;21(4):285–297. doi: 10.1097/CMR.0b013e32834495c3

Table 1. Distribution in functional categories of genes regulated by PEDF in A375 human melanoma cell line.

Selected relevant genes regulated by PEDFe are shown classified into functional categories described in the main text. Upregulated genes are included at the top of the list followed by downregulated genes. Shown are gene symbol, description and the linear ratio of GCRMA-normalized expression PEDF/control in the two hybridizations from independently isolated RNAs from A375-pCEP4-PEDF Pool y A375-pCEP4 Pool cells (Hybr. 1 and Hybr. 2).

ANGIOGENESIS/ADHESION/MIGRATION/INVASION
Gene symbol Description PEDF/Control
Hybr. 1 Hybr. 2
FN1 Fibronectin 1 14.22 16.52
VEGFC vascular endothelial growth factor C 3.13 4.64
FLT1 Fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor) 0.05 0.07
IL8 Interleukin 8 0.36 0.36
ITGB3 Integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61) 0.30 0.26
ITGB8 Integrin, beta 8 0.11 0.19
NRP2 Neuropilin 2 0.40 0.41
PCDH10 Protocadherin 10 0.10 0.12
PCDH17 Protocadherin 17 0.34 0.27
PCDHA9 Protocadherin alpha 9 0.46 0.48
PCDHB7 Protocadherin beta 7 0.34 0.34
PELO Integrin, alpha 1 0.12 0.15
TGFA Transforming growth factor, alpha 0.03 0.04
TGFBI Transforming growth factor, beta-induced, 68kDa 0.41 0.43
PROTEASES
Gene symbol Description PEDF/Control
Hybr. 1 Hybr. 2
ADAMTS6 A disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 6 3.39 8.66
ADAM10 A disintegrin and metalloproteinase domain 10 0.46 0.46
ADAM12 A disintegrin and metalloproteinase domain 12 (meltrin alpha) 0.27 0.47
ADAM19 A disintegrin and metalloproteinase domain 19 (meltrin beta) 0.06 0.09
ADAM23 A disintegrin and metalloproteinase domain 23 0.08 0.10
CTSH Cathepsin H 0.17 0.30
CTSK Cathepsin K (pycnodysostosis) 0.08 0.10
PLAT Plasminogen activator, tissue 0.39 0.40
PRSS11 protease, serine, 11 (IGF binding) 0.07 0.04
SERPINA3 Serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 0.05 0.04
SERPIND1 Serine (or cysteine) proteinase inhibitor, clade D (heparin cofactor), member 1 0.07 0.07
TIMP1 Tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor) 0.33 0.32
MELANIN SECRETION
Gene symbol Description PEDF/Control
Hybr. 1 Hybr. 2
MLPH Melanophilin 15.70 28.90
RAB27A RAB27A, member RAS oncogene family 0.31 0.22
MELANOMA PROGRESSION
Gene symbol Description PEDF/Control
Hybr. 1 Hybr. 2
DKK1 Dickkopf homolog 1 (Xenopus laevis) 2.86 2.87
DKK3 Dickkopf homolog 3 (Xenopus laevis) 2.28 2.85
FZD2 Frizzled homolog 2 (Drosophila) 2.60 2.38
FGF13 Fibroblast growth factor 13 0.14 0.08
FZD1 Frizzled homolog 1 (Drosophila) 0.37 0.42
GAGE1 G antigen 1 0.35 0.46
GAGE2 G antigen 2 0.11 0.10
GAGE4 G antigen 4 0.45 0.38
GAGE5 G antigen 5 0.24 0.31
IGFBP3 Insulin-like growth factor binding protein 3 0.11 0.22
INHBA Inhibin, beta A (activin A, activin AB alpha polypeptide) 0.18 0.24
JAG1 Jagged 1 (Alagille syndrome) 0.14 0.13
LEF1 Lymphoid enhancer-binding factor 1 0.48 0.37
LGALS3 Lectin, galactoside-binding, soluble, 3 (galectin 3) /// galectin-3 internal gene 0.23 0.21
NOTCH2NL Notch homolog 2 (Drosophila) N-terminal like 0.29 0.26
MELANOMA MARKERS
Gene symbol Description PEDF/Control
Hybr. 1 Hybr. 2
MAGEA1 Melanoma antigen family A, 1 (directs expression of antigen MZ2-E) 2.78 2.78
CSPG4 Chondroitin sulfate proteoglycan 4 (melanoma-associated) 0.19 0.24
MIA Melanoma inhibitory activity 0.48 0.44
S100A1 S100 calcium binding protein A1 0.33 0.13
S100A13 S100 calcium binding protein A13 0.38 0.33
S100A16 S100 calcium binding protein A16 0.29 0.36
S100A2 S100 calcium binding protein A2 0.30 0.27
S100A3 S100 calcium binding protein A3 0.15 0.12
S100A4 S100 calcium binding protein A4 (calcium protein, calvasculin, metastasin, murine placental homolog) 0.10 0.09
S100B S100 calcium binding protein, beta (neural) 0.13 0.10
TRANSCRIPTION FACTORS
Gene symbol Description PEDF/Control
Hybr. 1 Hybr. 2
FOXF2 Forkhead box F2 2.16 2.32
SOX11 SRY (sex determining region Y)-box 11 3.85 4.10
SOX9 SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal) 2.27 12.34
NFATC2 Nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 0.29 0.22
SOX2 SRY (sex determining region Y)-box 2 0.41 0.46
SOX5 SRY (sex determining region Y)-box 5 0.20 0.08
TBX2 T-box 2 0.24 0.19
APOPTOSIS
Gene symbol Description PEDF/Control
Hybr. 1 Hybr. 2
BID BH3 interacting domain death agonist 2.17 2.28
NGFR Nerve growth factor receptor (TNFR superfamily, member 16) 6.67 4.56
ARHGEF6 Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 0.46 0.23
BCL2A1 BCL2-related protein A1 0.04 0.05
BIRC3 Baculoviral IAP repeat-containing 3 0.36 0.18
FAIM3 Fas apoptotic inhibitory molecule 0.32 0.30
FAS Fas (TNF receptor superfamily, member 6) 0.19 0.19
TNFSF7 Tumor necrosis factor (ligand) superfamily, member 7 0.33 0.35
CELL PROLIFERATION
Gene symbol Description PEDF/Control
Hybr. 1 Hybr. 2
CCNJ Cyclin J 2.04 2.91
CLEC11A C-type lectin domain family 11, member A 3.94 3.52
CYR61 Cysteine-rich, angiogenic inducer, 61 2.06 2.55
E2F5 E2F transcription factor 5, p130-binding 3.72 3.91
HDAC9 Histone deacetylase 9 2.51 3.35
MDK Midkine (neurite growth-promoting factor 2) 7.29 9.42
CCNA1 Cyclin A1 0.10 0.08
CDKN1A Cyclin-dependent kinase inhibitor 1A (p21, Cip1) 0.21 0.37
DUSP4 Dual specificity phosphatase 4 0.39 0.32
HIPK2 Homeodomain interacting protein kinase 2 0.41 0.41
IGF1R Insulin-like growth factor 1 receptor 0.25 0.25
IGFBP2 Insulin-like growth factor binding protein 2, 36kDa 0.24 0.14
IGFBP5 Insulin-like growth factor binding protein 5 0.27 0.27
IGFBP7 Insulin-like growth factor binding protein 7 0.32 0.45
NDN Necdin homolog (mouse) 0.07 0.09
CYTOKINES
Gene symbol Description PEDF/Control
Hybr. 1 Hybr. 2
IL13RA2 Interleukin 13 receptor, alpha 2 0.41 0.44
IL1A Interleukin 1, alpha 0.16 0.11
IL1RAP Interleukin 1 receptor accessory protein 0.17 0.14
IL24 Interleukin 24 0.06 0.07
IL6ST Interleukin 6 signal transducer (gp130, oncostatin M receptor) 0.38 0.38
METABOLISM
Gene symbol Description PEDF/Control
Hybr. 1 Hybr. 2
PLTP phospholipid transfer protein 2.73 2.71
ACOX2 acyl-Coenzyme A oxidase 2, branched chain 0.49 0.30
ACSL1 acyl-CoA synthetase long-chain family member 1 0.34 0.39
ADPGK ADP-dependent glucokinase 0.39 0.38
B3GAT1 beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P) 0.35 0.29
CHST11 carbohydrate (chondroitin 4) sulfotransferase 11 0.36 0.18
IRS2 insulin receptor substrate 2 0.44 0.40
MGLL monoglyceride lipase /// monoglyceride lipase 0.24 0.44
PLA2G4A phospholipase A2, group IVA (cytosolic, calcium-dependent) 0.24 0.38