Table 3.
Head and Neck Squamous Cell Carcinoma | Oral Cavity SquamousCell Carcinoma | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Ginos Dataset | Cromer Dataset | Peng Dataset | Toruner dataset | |||||||
Cancer vs. Normal | Cancer vs. Normal | Cancer vs. Normal | Cancer vs. Normal | |||||||
n | Protein | Gene | Fold Change | p Value | Fold Change | p Value | Fold Change | p Value | Fold Change | p Value |
1 | p16INK4a | CDKN2A | 2.297 | 6.27 × 10−5 | −1.415 | 0.712 | 1.684 | 1.21 × 10−7 | 1.372 | 0.047 |
p16INK4a Downstream Genes | ||||||||||
2 | CDK4 | CDK4 | 1.842 | 8.84 × 10−12 | 2.63 | 8.00 × 10−6 | 1.498 | 3.76E−08 | 2.13 | 6.31 × 10−4 |
3 | Cyclin D1 | CCND1 | 1.465 | 0.023 | 2.031 | 5.97 × 10−5 | −1.112 | 0.907 | 1.201 | 0.164 |
4 | pRB | RB1 | 1.372 | 8.92 × 10−4 | 1.165 | 0.429 | 1.2 | 0.018 | 1.579 | 0.005 |
5 | p107 | RBL1 | n.a. | n.a. | −2.032 | 0.97 | 1.334 | 4.47 × 10−4 | n.a. | n.a. |
6 | p130 | RBL2 | 1.081 | 0.172 | −1.449 | 0.774 | −1.228 | 0.997 | 1.141 | 0.046 |
7 | E2F1 | E2F1 | 1.347 | 0.046 | 1.754 | 1.00 × 10−6 | 1.032 | 0.313 | 1.083 | 0.05 |
8 | E2F2 | E2F2 | −1.329 | 0.856 | −1.147 | 0.813 | −1.424 | 1 | 1.044 | 0.172 |
9 | E2F3 | E2F3 | 2.945 | 7.20 × 10−8 | 1.948 | 0.159 | 1.099 | 4.19 × 10−15 | 1.231 | 0.284 |
10 | E2F4 | E2F4 | 1.131 | 0.025 | 1.462 | 0.014 | 1.415 | 1.28 × 10−11 | −1.178 | 1.00 |
Epigenetic Regulator Genes | ||||||||||
11 | DNMT1 | DNMT1 | 1.706 | 2.00 × 10−7 | 1.581 | 0.124 | 1.499 | 1.87 × 10−15 | 1.457 | 2.00 × 10−3 |
12 | DNMT3A | DNMT3A | −1.046 | 0.584 | n.a. | n.a. | 1.01 | 0.37 | −1.038 | 0.644 |
13 | DNMT3B | DNMT3B | 1.37 | 5.19 × 10−4 | n.a. | n.a. | 1.512 | 3.82 × 10−8 | 1.296 | 0.009 |
14 | Bmi-1 | BMI1 | 1.818 | 3.23 × 10−7 | 1.627 | 5.16 × 10−5 | −1.046 | 0.689 | 1.708 | 2.78 × 10−7 |
15 | Ezh1 | EZH1 | 1.238 | 0.011 | 1.383 | 0.083 | 1.131 | 6.00 × 10−2 | 1.259 | 0.03 |
16 | Ezh2 | EZH2 | −1.325 | 0.88 | −1.151 | 0.833 | −1.401 | 1.000 | 1.021 | 0.4 |
17 | EED | EED | 1.495 | 3.89 × 10−4 | 1.118 | 0.286 | 1.349 | 3.12 × 10−7 | 1.112 | 0.013 |
18 | CBX4 | CBX4 | −1.133 | 0.750 | −1.132 | 0.613 | −1.183 | 0.999 | −1.04 | 0.817 |
19 | CBX7 | CBX7 | −1.429 | 0.992 | n.a. | n.a. | −1.311 | 1 | −1.24 | 1 |
20 | Jarid2 | JARID2 | 1.123 | 0.045 | 1.17 | 0.039 | 1.2 | 0.002 | 1.365 | 0. 948 |
21 | JMJD3 | JMJD3 | 1.039 | 0.292 | 1.127 | 0.116 | 1.088 | 0.174 | −1.229 | 0.924 |
22 | JDP2 | JDP2 | n.a. | n.a. | n.a. | n.a. | −1.214 | 1 | n.a. | n.a. |
23 | SETD8 | KMT5A | −1.375 | 0.999 | n.a. | n.a. | 1.058 | 0.214 | 1.097 | 2.19 × 10−4 |
24 | KMT2A | MLL | −1.185 | 0.974 | −1.252 | 0.901 | 1.179 | 0.005 | 1.11 | 0.215 |
25 | HAT p300 | EP300 | 1.054 | 0.327 | −1.196 | 0.737 | 1.141 | 0.006 | −1.146 | 0.904 |
26 | HDAC | HDAC1 | −1.075 | 0.83 | 1.361 | 0.054 | 1.174 | 0.016 | 1.883 | 1.42 × 10−4 |
27 | HDAC | HDAC2 | 1.613 | 1.41 × 10−4 | 1.181 | 0.241 | 1.066 | 0.151 | 1.265 | 0.029 |
28 | p63 | TP63 | 1.491 | 0.001 | 1.717 | 0.019 | 1.238 | 2.68 × 10−4 | 1.12 | 0.021 |
29 | BRG1 | SMARCA4 | 1.047 | 0.309 | −1.543 | 0.960 | 1.001 | 0.416 | 1.175 | 9.28 × 10−4 |
30 | LSH | HELLS | 2.463 | 0.013 | n.a. | n.a. | 1.617 | 6.24 × 10−6 | 1.445 | 0.004 |
31 | Satb1 | SATB1 | 1.025 | 0.396 | −2.039 | 0.92 | −1.496 | 0.997 | −1.685 | 1 |
32 | CTCF | CTCF | 1.003 | 0.478 | 1.292 | 0.018 | −1.114 | 0.998 | 1.29 | 0.097 |
Transcriptional Regulator Genes | ||||||||||
33 | Ets1 | ETS1 | 1.694 | 0.001 | 2.076 | 0.016 | 2.111 | 2.97 × 10−10 | −1.114 | 1 |
34 | Ets2 | ETS2 | 1.78 | 1.76 × 10−6 | 1.761 | 0.012 | −1.102 | 0.908 | −1.218 | 0.618 |
35 | ID1 | ID1 | 1.356 | 0.015 | 1.375 | 0.278 | 1.21 | 0.025 | 1.242 | 0.317 |
36 | ID2 | ID2 | 1.765 | 1.79 × 10−4 | 2.022 | 0.258 | 1.066 | 0.193 | 1.038 | 0.362 |
37 | ID3 | ID3 | 3.023 | 2.14 × 10−4 | n.a. | n.a. | 1.072 | 0.208 | 1.043 | 0.447 |
38 | YB1 | YXB1 | 1.421 | 0.001 | 1.644 | 6.26 × 10−4 | −1.362 | 0.998 | 1.637 | 0.001 |
39 | SP1 | SP1 | 1.292 | 0.95 | −1.382 | 0.717 | −1.232 | 1 | 1.008 | 0.372 |
40 | HBP1 | PBRM1 | −1.131 | 0.716 | n.a. | n.a. | −1.303 | 1.00 | 1.039 | 0.137 |
41 | b-myb | MYB | 1.003 | 0.495 | 1.414 | 0.13 | −1.842 | 1 | 1.134 | 0.229 |
42 | JUNB | JUNB | 1.38 | 0.006 | 1.252 | 0.093 | 1.003 | 0.485 | −1.029 | 0.552 |
43 | c-Jun | C-JUN | 1.549 | 1.13 × 10−5 | 1.18 | 0.083 | 1.318 | 0.008 | −1.093 | 0.508 |
44 | JunD | JUND | −1.048 | 0.549 | 1.176 | 0.05 | −1.227 | 0.999 | 1.045 | 0.086 |
45 | c-Fos | C-FOS | 13.503 | 2.88 × 10−5 | 1.481 | 0.212 | −1.415 | 0.956 | 1.225 | 0.365 |
46 | FosB | FOSB | 3.016 | 0.005 | 1.385 | 0.021 | −1.042 | 0.527 | −1.881 | 1 |
47 | FRA1 | FOSL1 | 1.663 | 0.076 | −1.194 | 0.922 | 1.2 | 0.045 | −3.719 | 0.946 |
48 | FRA2 | FOSL2 | −1.355 | 0.997 | 1.13 | 0.205 | −2.032 | 1 | −1.149 | 0.909 |
49 | PPARalpha | PPARA | −1.043 | 0.406 | −1.134 | 0.585 | −1.079 | 0.984 | 1.021 | 0.104 |
50 | ANRIL | CDKN2BAS | n.a. | n.a. | n.a. | n.a. | 1.802 | 8.85 × 10−12 | n.a. | n.a. |
The table shows the tumors types, dataset names, and complete list of genes investigated in the present study, from Oncomine database (www.oncomine.org). Statistically significant expression fold changes (p ≤ 0.05) are labeled: fold change ≥ 2 (green); fold change < 2 (light green); n.a.: not available data.