Table I.
Significantly deregulated genes that are differentially expressed in comparisons of MAFs, ACFs and CDFs.
| A, Upregulated genes, MAF vs. CDF
| |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Entrez gene ID | EnsEMBL gene ID | Symbol | Definition | Descriptive GO BP term | FDR | CDF log2-intensity | MAF log2-intensity | ACF log2-intensity | |
| 3036 | ENSG00000105509 | HAS1 | Hyaluronan synthase 1 | GO:0085029 | 8E-23 | 4.50 | 7.62 | 4.50 | |
| 221303 | ENSG00000183807 | FAM162B | Family with sequence similarity 162, member B | – | 3E-22 | 4.48 | 7.85 | 5.10 | |
| 3875 | ENSG00000111057 | KRT18 | Keratin 18 | GO:0009653 | 2E-20 | 5.45 | 9.76 | 8.93 | |
| 894 | ENSG00000118971 CC | ND2 | Cyclin D2 | GO:0008284 | 2E-20 | 5.00 | 9.10 | 6.85 | |
| 8076 | ENSG00000197614 | MFAP5 | Microfibrillar associated protein 5 | GO:0030198a | 2E-19 | 7.73 | 12.06 | 12.24 | |
| 11341 | ENSG00000164106 | SCRG1 | Stimulator of chondrogenesis 1 | GO:0007399 | 2E-19 | 4.55 | 8.26 | 7.07 | |
| 5909 | ENSG00000076864 | RAP1GAP | RAP1 GTPase activating protein | GO:0043087 | 2E-19 | 4.50 | 7.59 | 5.10 | |
| 353139 | ENSG00000187173 | LCE2A | Late cornified envelope 2A | GO:0030216 | 3E-19 | 4.96 | 7.77 | 5.34 | |
| 1776 | ENSG00000163687 D | NASE1L3 | Deoxyribonuclease I-like 3 | GO:0006309 | 7E-18 | 4.56 | 7.51 | 5.79 | |
| 284085 | ENSG00000265480 | KRT18P55 | Keratin 18 pseudogene 55 | – | 1E-17 | 4.68 | 8.37 | 7.04 | |
| 3202 | ENSG00000106004 | HOXA5 | Homeobox A5 | GO:0048704a | 2E-17 | 7.30 | 10.72 | 7.39 | |
| 1829 | ENSG00000046604 D | SG2 | Desmoglein 2 | GO:0007155 | 6E-17 | 4.65 | 7.78 | 4.92 | |
| 3887 | ENSG00000205426 | KRT81 | keratin 81 | GO:0005198 | 7E-17 | 5.67 | 8.93 | 6.94 | |
| B, Downregulated genes, MAF vs. CDF
| ||||||||
|---|---|---|---|---|---|---|---|---|
| Entrez gene ID | EnsEMBL gene ID | Symbol | Definition | Descriptive GO BP term | FDR | CDF log2-intensity | MAF log2-intensity | ACF log2-intensity |
| 404266 | ENSG00000233101 | HOXB-AS3 | HOXB cluster antisense RNA 3 (non- protein coding) | – | 2E-21 | 9.54 | 5.92 | 9.78 |
| 8988 | ENSG00000169271 | HSPB3 | Heat shock 27 kDa protein 3 | GO:0006986 | 6E-18 | 10.12 | 5.73 | 9.35 |
| 6387 | ENSG00000107562 C | XCL12 | Chemokine (C-X-C motif) ligand 12 | GO:0001666a | 9E-18 | 10.36 | 4.97 | 10.19 |
| 1396 | ENSG00000213145 C | RIP1 | Cysteine-rich protein 1 (intestinal) | GO:0008283 | 1E-17 | 11.03 | 7.10 | 8.73 |
| 160364 | ENSG00000172322 | CLEC12A | C-type lectin domain family 12, member A | – | 2E-17 | 5.99 | 4.53 | 4.48 |
| 4147 | ENSG00000132561 | MATN2 | Matrilin 2 | GO:0008347a | 5E-17 | 10.57 | 6.86 | 9.11 |
| 160364 | ENSG00000172322 | CLEC12A | C-type lectin domain family 12, member A, transcript variant 2 | – | 8E-17 | 6.64 | 4.51 | 4.55 |
| C, Upregulated genes, MAF vs. ACF
| ||||||||
|---|---|---|---|---|---|---|---|---|
| Entrez gene ID | EnsEMBL gene ID | Symbol | Definition | Descriptive GO BP term | FDR | CDF log2-intensity | MAF log2-intensity | ACF log2-intensity |
| 3036 | ENSG00000105509 | HAS1 | Hyaluronan synthase 1 | GO:0085029 | 1E-22 | 4.50 | 7.62 | 4.50 |
| 221303 | ENSG00000183807 | FAM162B | Family with sequence similarity 162, member B | – | 3E-19 | 4.48 | 7.85 | 5.10 |
| 3202 | ENSG00000106004 | HOXA5 | Homeobox A5 | GO:0048704a | 7E-17 | 7.30 | 10.72 | 7.39 |
| 353139 | ENSG00000187173 | LCE2A | Late cornified envelope 2A | GO:0030216 | 1E-16 | 4.96 | 7.77 | 5.34 |
| 5909 | ENSG00000076864 | RAP1GAP | RAP1 GTPase activating protein | GO:0043087 | 5E-16 | 4.50 | 7.59 | 5.15 |
| 1829 | ENSG00000046604 D | SG2 | Desmoglein 2 | GO:0007155 | 5E-15 | 4.65 | 7.78 | 4.92 |
| 55966 | ENSG00000196581 | AJAP1 | Adherens junctions associated protein 1 | GO:0007155 | 1E-13 | 4.60 | 6.16 | 4.37 |
| 1300 | ENSG00000123500 C | OL10A1 | Collagen, type X, α1 | GO:0030198a | 2E-14 | 5.11 | 7.78 | 4.93 |
| 3778 | ENSG00000156113 | KCNMA1 | Potassium large conductance calcium- activated channel, subfamily M, α member 1 | GO:0001666a | 2E-14 | 9.64 | 9.46 | 6.95 |
| 794 | ENSG00000172137 C | ALB2 | Calbindin 2 | GO:0005509 | 8E-14 | 6.78 | 8.33 | 4.98 |
| D, Downregulated genes, MAF vs. ACF
| ||||||||
|---|---|---|---|---|---|---|---|---|
| Entrez gene ID | EnsEMBL gene ID | Symbol | Definition | Descriptive GO BP term | FDR | CDF log2-intensity | MAF log2-intensity | ACF log2-intensity |
| 404266 | ENSG00000233101 | HOXB-AS3 | HOXB cluster antisense RNA 3 (non-protein coding) | – | 3E-21 | 9.54 | 5.92 | 9.78 |
| 116154 | ENSG00000087495 | PHACTR3 | Phosphatase and actin regulator 3 | GO:0043086 | 2E-19 | 7.40 | 5.32 | 10.49 |
| 72 | ENSG00000163017 | ACTG2 | Actin, γ2, smooth muscle, enteric | GO:0090131 | 2E-18 | 4.84 | 4.58 | 12.18 |
| 70 | ENSG00000159251 | ACTC1 | Actin, α, cardiac muscle 1 | GO:0090131 | 7E-17 | 9.89 | 7.27 | 12.76 |
| 6387 | ENSG00000107562 C | XCL12 | Chemokine (C-X-C motif) ligand 12 | GO:0001666a | 7E-17 | 10.36 | 4.97 | 10.19 |
| 154197 | ENSG00000146453 | PNLDC1 | Poly(A)-specific ribonuclease (PARN)-like domain containing 1 | – | 3E-16 | 4.49 | 4.45 | 5.51 |
| 8988 | ENSG00000169271 | HSPB3 | Heat shock 27 kDa protein 3 | GO:0006986 | 8E-15 | 10.12 | 5.73 | 9.35 |
| 90139 | ENSG00000157570 | TSPAN18 | Tetraspanin 18 | GO:0030198 | 8E-15 | 5.69 | 4.90 | 8.26 |
| 668 | ENSG00000183770 | FOXL2 | Forkhead box L2 | GO:0030154 | 3E-14 | 7.66 | 4.79 | 8.16 |
| 5121 | ENSG00000183036 | PCP4 | Purkinje cell protein 4 | GO:0007417 | 1E-13 | 4.53 | 4.44 | 7.16 |
| E, Upregulated genes, ACF vs. CDF
| ||||||||
|---|---|---|---|---|---|---|---|---|
| Entrez gene ID | EnsEMBL gene ID | Symbol | Definition | Descriptive GO BP term | FDR | CDF log2-intensity | MAF log2-intensity | ACF log2-intensity |
| 8076 | ENSG00000197614 | MFAP5 | Microfibrillar associated protein 5 | GO:0030198a | 2E-18 | 7.73 | 12.06 | 12.24 |
| 72 | ENSG00000163017 | ACTG2 | Actin, γ2, smooth muscle, enteric | GO:0090131 | 4E-17 | 4.84 | 4.58 | 12.18 |
| 3875 | ENSG00000111057 | KRT18 | Keratin 18 | GO:0009653 | 4E-16 | 5.45 | 9.76 | 8.93 |
| 85409 | ENSG00000145506 | NKD2 | Naked cuticle homolog 2 (Drosophila) | GO:0030178 | 7E-16 | 4.45 | 7.27 | 7.70 |
| 154197 | ENSG00000146453 | PNLDC1 | Poly(A)-specific ribonuclease (PARN)-like domain containing 1 | – | 2E-15 | 4.49 | 4.45 | 5.51 |
| 8322 | ENSG00000174804 | FZD4 | Frizzled family receptor 4 | GO:0060070 | 3E-15 | 6.85 | 8.31 | 9.66 |
| 64798 | ENSG00000155792 | DEPTOR | DEP domain containing MTOR-interacting protein | GO:0035556 | 1E-13 | 4.79 | 6.71 | 8.64 |
| 11341 | ENSG00000164106 | SCRG1 | Stimulator of chondrogenesis 1 | GO:0007399 | 2E-13 | 4.55 | 8.26 | 7.07 |
| 54518 | ENSG00000077420 | APBB1IP | Amyloid beta (A4) precursor protein-binding. family B, member 1 interacting protein | GO:0045785a | 2E-13 | 7.60 | 9.39 | 9.57 |
| 157506 | ENSG00000121039 | RDH10 | Retinol dehydrogenase 10 (all-trans) | GO:0014032 | 3E-13 | 7.38 | 9.37 | 10.58 |
| 5121 | ENSG00000183036 | PCP4 | Purkinje cell protein 4 | GO:0007417 | 3E-13 | 4.53 | 4.44 | 7.16 |
| 3751 | ENSG00000184408 | KCND2 | Potassium voltage-gated channel. Shal-related subfamily, member 2 | GO:0071456 | 3E-13 | 4.42 | 6.28 | 6.14 |
| F, Downregulated genes, ACF vs. CDF
| ||||||||
|---|---|---|---|---|---|---|---|---|
| Entrez gene ID | EnsEMBL gene ID | Symbol | Definition | Descriptive GO BP term | FDR | CDF log2-intensity | MAF log2-intensity | ACF log2-intensity |
| 4885 | ENSG00000106236 | NPTX2 | Neuronal pentraxin II | – | 4E-17 | 9.10 | 6.41 | 5.30 |
| 100133941 | ENSG00000272398 | CD24 | CD24 molecule | GO:0002237a | 3E-16 | 10.02 | 7.09 | 6.68 |
| 160364 | ENSG00000172322 | CLEC12A | C-type lectin domain family 12. member A | – | 4E-16 | 5.99 | 4.53 | 4.48 |
| 160364 | ENSG00000172322 | CLEC12A | C-type lectin domain family 12. member A. transcript variant 2 | – | 1E-15 | 6.64 | 4.51 | 4.55 |
| 3778 | ENSG00000156113 | KCNMA1 | Potassium large conductance calcium-activated channel. Subfamily M. α member 1 | GO:0001666a | 9E-15 | 9.64 | 9.46 | 6.95 |
| 84675 | ENSG00000147573 | TRIM55 | Tripartite motif containing 55 | GO:0007165 | 3E-13 | 6.31 | 4.70 | 4.47 |
| 6228 | ENSG00000186468 | RPS23 | Ribosomal protein S23 | GO:0005840 | 6E-13 | 11.47 | 8.85 | 8.83 |
| 85352 | ENSG00000138944 | KIAA1644 | KIAA1644 | – | 7E-13 | 9.68 | 6.61 | 7.14 |
The 20 most marked DEGs are listed.
a
Listed among GO terms enriched by DEGs as identified by gene set enrichment analysis. Significance level, FDR<0.05. MAF, melanoma-associated fibroblast; ACF, autologous control fibroblast; CDF, control dermal fibroblast; FDR, false discovery rate; DEG, differentially expressed gene; GO BP, gene ontology biological process.