Table 2.
Genes regulated by promoter regulation: A. 26 genes overexpressed in CAF compared to NF.
| Function | Probeset | Gene name | Gene Symbol |
Fold Change |
P value |
|---|---|---|---|---|---|
| Metabolism/Transport | cg13077930 | Albumin | ALB | 1.71E+18 | 0.000272652 |
| cg26984624 | Ankrin 1, erythrocytic | ANK1 | 3.48E+07 | 0.00736581 | |
| cg20857947 | Arginisuccinate lyase | ASL | 121184 | 0.027152 | |
| cg22063653 | 2,3 bisphosphoglycerate mutase | BPGM | 28981.8 | 0.0218035 | |
| cg09425611 | Carboxylesterase 1 | CES1 | 431.142 | 0.0358082 | |
| cg00901704 | Solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19 | SLC25A19 | 1.83E+27 | 0.0170674 | |
| cg08724474 | Solute carrier family 36 (proton/amino acid symporter), member 1 | SLC36A1 | 1.77E+36 | 0.0304509 | |
| cg14265670 | Uridine phosphorylase 1 | UPP1 | 2.91E+07 | 0.0365465 | |
| cg18412613 | YKT6-v-SNARE homolog | YKT6 | 478304 | 0.0461634 | |
| cg14493899 | Transporter 2, ATP-binding cassette, subfamily B (MDR/TAP) | TAP2 | 2.17E+14 | 0.0232357 | |
| Adhesion/Signaling | cg01288598 | CD83 molecule | CD83 | 68474.7 | 0.0271523 |
| cg05649009 | Cholinergic receptor, nicotinic, alpha1 (muscle) | CHRNA1 | 4.72E+27 | 0.049423 | |
| cg11552293 | Collagen, type IV, alpha 6 | COL4A6 | 1067.49 | 0.030782 | |
| cg11393453 | GRB2 associated regulator of MAPK1 | FAM59A | 1.61E+10 | 0.0329179 | |
| cg13060405 | Myosin XVIIIA | MYO18A | 1.43E+27 | 0.0304239 | |
| cg25187533 | Pregnancy specific beta-1-glycoprotein 2 | PSG2 | 1.13E+32 | 0.000976575 | |
| cg00950418 | SRSF protein kinase 2 | SRPK2 | 1.41E+10 | 0.0240908 | |
| Cell cycle | cg25522312 | MAD2 mitotic arrest deficient-like 1 (yeast) | MAD2L1 | 3.81E+07 | 0.0084277 |
| cg08062469 | Sperm associated antigen 5 | SPAG5 | 4.13E+09 | 0.0369162 | |
| cg19738333 | Receptor accessory protein 4 | REEP4 | 6.08E+12 | 0.018247 | |
| Transcription | cg20150743 | Zinc finger protein 3 | ZNF3 | 9578.43 | 0.0128924 |
| Autophagy | cg10732834 | Ectopic P-granules autophagy protein 5 homolog (C. elegans) | KIAA1632 | 5.03E+33 | 0.0311191 |
| Unknown | cg22010317 | chromosome X open reading frame 36 | Cxorf36 | 43048.4 | 0.0126714 |
| cg17178888 | FLJ14166 | 7.39E+07 | 0.0392013 | ||
| cg02890926 | Transmembrane protein 53 | TMEM53 | 1.40E+06 | 0.02627 | |
| cg25861458 | FL23356 | 130539 | 0.00114061 |
| B. 33 Genes under-expressed in CAF compared to NF | |||||
|---|---|---|---|---|---|
| Function | Probeset | Gene name | Gene Symbol |
Fold Change |
P value |
| Signaling | cg22930187 | Artemin | ARTN | −4008.21 | 0.0195053 |
| cg04929736 | Clusterin | CLU | −1.21E+14 | 0.0126985 | |
| cg03278643 | Ellis van Creveld syndrome 2 | EVC2 | −9.16E+06 | 0.022855 | |
| cg24888049 | Feline sarcoma oncogene | FES | −1.31E+29 | 0.005809 | |
| cg18977436 | Fibroblast growth factor 14 | FGF14 | −68717.7 | 0.025556 | |
| cg24222324 | Tumor necrosis factor superfamily, member 11 | TNFSF11 | −2227.31 | 0.008463 | |
| cg11072113 | von Willebrand factor C and EGF domains | VWCE | −1.21E+18 | 0.049167 | |
| Cell-cell; cytoskeletal | cg02512860 | Claudin 15 | CLDN15 | −37932.3 | 0.025022 |
| cg06799664 | Dynein, axonemal, heavy chain like 1 | DNAHL1 | −6381.26 | 0.044435 | |
| cg07126559 | Sarcoglycan, gamma (35kDa dystrophinassociated glycoprotein) | SGCG | −6.45E+29 | 0.03913 | |
| Enzyme | cg22333888 | ADAM metallopeptidase domain 33 | ADAM33 | −1.33E+29 | 0.0146697 |
| cg23026995 | X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound | XPNPEP2 | −2.29E+23 | 0.030756 | |
| Transcription factors | cg19556572 | AT-hook transcription factor | AKNA | −5.29E+35 | 0.007186 |
| cg10003443 | forkhead box A2 | FOXA2 | −7451.05 | 0.012987 | |
| cg08789630 | K(lysine) acetyltransferase 6B | MYST4 | −1.74E+07 | 0.029483 | |
| cg16722536 | T-box 1 | TBX1 | −17684 | 0.020172 | |
| cg12788467 | HNF1 homeobox B | TCF2 | −2542.91 | 0.037723 | |
| cg19352038 | Paired box 3 | PAX3 | −27179.6 | 0.013469 | |
| cg07403255 | Paired box 8 | PAX8 | −6.64E+06 | 0.022095 | |
| Apoptosis | cg06493930 | Growth arrest-specific 2 | GAS2 | −699.226 | 0.021412 |
| cg05924583 | Tumor protein p73 | TP73 | −211.453 | 0.027257 | |
| Transport | cg27461196 | FXYD domain containing ion transport regulator 1 | FXYD1 | −1.94E+21 | 0.048906 |
| cg04502814 | Selenoprotein P, plasma, 1 | SEPP1 | −1.24E+13 | 0.033794 | |
| cg16509045 | transient receptor potential cation channel, subfamily M, member 6 | TRPM6 | −600.168 | 0.030977 | |
| Metabolism | cg10432859 | UDP glucuronosyltransferase 1 family, polypeptide A7 | UGT1A7 | −11322.6 | 0.017452 |
| Unknown | cg01813965 | Coiled-coil domain containing 135 | C16orf50 | −9979.22 | 0.009274 |
| cg18752880 | C1q and tumor necrosis factor related protein 3 | C1QTNF3 | −1.03E+06 | 0.028981 | |
| cg24691461 | cerebral cavernous malformation 2-like, CCM2L | C20orf160 | −4898.6 | 0.00563 | |
| cg02654291 | chromosome 9 open reading frame 64 | C9orf64 | −254582 | 0.016801 | |
| cg21489873 | MIR600 host gene (non-protein coding) | C9orf45 | −2.41E+19 | 0.049695 | |
| cg15679095 | GLTSCR1-like | KIAA0240 | −6.85E+31 | 0.034122 | |
| cg02077702 | immunoglobulin superfamily containing leucine-rich repeat | ISLR | −1.13E+23 | 0.030866 | |
| cg19170321 | Calpain 3, p94 | CAPN3 | −4.66E+13 | 0.0233799 | |