The two-gene combinations with highest frequency as cSEG markers in 13 cancers
| Cancer . | Gene 1 . | Gene 1 frequency . | Gene 2 . | Gene 2 frequency . | Co-frequency . | P-value of two-gene combination . |
|---|---|---|---|---|---|---|
| BLCA | FER1L4 | 54% | SHISA5 | 66% | 75% | 5.07E-10 |
| BRCA | GALNT6 | 58% | GATA3 | 63% | 75% | 3.44E-17 |
| CESC | KLHDC7B | 55% | TCAM1P | 61% | 84% | 1.19E-14 |
| CHOL | ARRDC2 | 61% | ANXA9 | 64% | 81% | 0.12 |
| CHOL | ARRDC2 | 61% | GMNN | 58% | 81% | 0.07 |
| CHOL | ARRDC2 | 61% | SLFN13 | 64% | 81% | 0.12 |
| HNSC | LAMB3 | 60% | ALOXE3 | 56% | 80% | 1.10E-16 |
| HNSC | LAMB3 | 60% | TM4SF19 | 56% | 80% | 1.10E-16 |
| HNSC | DNAH17 | 54% | ITGA6 | 61% | 80% | 6.16E-19 |
| KICH | ACO2 | 82% | ARSJ | 58% | 97% | 2.08E-07 |
| KICH | ACO2 | 82% | CLNK | 68% | 97% | 0.000036 |
| KICH | DLAT | 70% | OGDH | 83% | 97% | 0.000072 |
| KICH | ELOVL7 | 67% | PPDPF | 70% | 97% | 0.000018 |
| KIRC | NRP1 | 69% | FBXO17 | 70% | 89% | 1.81E-15 |
| KIRC | NRP1 | 69% | HMOX1 | 66% | 89% | 4.23E-19 |
| KIRC | NRP1 | 69% | SPAG4 | 67% | 89% | 1.05E-17 |
| KIRC | FLT1 | 63% | SPAG4 | 67% | 89% | 5.16E-23 |
| KIRP | C2orf18 | 65% | CREB5 | 62% | 92% | 1.07E-17 |
| KIRP | C2orf18 | 65% | ITM2B | 74% | 92% | 3.46E-15 |
| LIHC | AKR1C3 | 60% | EFNA1 | 65% | 83% | 6.12E-12 |
| PRAD | ERGIC1 | 79% | CREB3L1 | 67% | 91% | 4.22E-20 |
| PRAD | ERGIC1 | 79% | DNAH8 | 59% | 91% | 6.43E-31 |
| SKCM | ABL2 | 65% | HMCN1 | 58% | 83% | 3.99E-17 |
| THCA | S100A13 | 73% | SLC17A5 | 67% | 88% | 2.32E-15 |
| THCA | S100A13 | 73% | LTBP3 | 66% | 88% | 1.81E-16 |
| UCEC | DLX5 | 56% | EYA2 | 58% | 79% | 5.64E-06 |
| UCEC | DLX5 | 56% | CAPS | 58% | 79% | 5.64E-06 |
| Cancer . | Gene 1 . | Gene 1 frequency . | Gene 2 . | Gene 2 frequency . | Co-frequency . | P-value of two-gene combination . |
|---|---|---|---|---|---|---|
| BLCA | FER1L4 | 54% | SHISA5 | 66% | 75% | 5.07E-10 |
| BRCA | GALNT6 | 58% | GATA3 | 63% | 75% | 3.44E-17 |
| CESC | KLHDC7B | 55% | TCAM1P | 61% | 84% | 1.19E-14 |
| CHOL | ARRDC2 | 61% | ANXA9 | 64% | 81% | 0.12 |
| CHOL | ARRDC2 | 61% | GMNN | 58% | 81% | 0.07 |
| CHOL | ARRDC2 | 61% | SLFN13 | 64% | 81% | 0.12 |
| HNSC | LAMB3 | 60% | ALOXE3 | 56% | 80% | 1.10E-16 |
| HNSC | LAMB3 | 60% | TM4SF19 | 56% | 80% | 1.10E-16 |
| HNSC | DNAH17 | 54% | ITGA6 | 61% | 80% | 6.16E-19 |
| KICH | ACO2 | 82% | ARSJ | 58% | 97% | 2.08E-07 |
| KICH | ACO2 | 82% | CLNK | 68% | 97% | 0.000036 |
| KICH | DLAT | 70% | OGDH | 83% | 97% | 0.000072 |
| KICH | ELOVL7 | 67% | PPDPF | 70% | 97% | 0.000018 |
| KIRC | NRP1 | 69% | FBXO17 | 70% | 89% | 1.81E-15 |
| KIRC | NRP1 | 69% | HMOX1 | 66% | 89% | 4.23E-19 |
| KIRC | NRP1 | 69% | SPAG4 | 67% | 89% | 1.05E-17 |
| KIRC | FLT1 | 63% | SPAG4 | 67% | 89% | 5.16E-23 |
| KIRP | C2orf18 | 65% | CREB5 | 62% | 92% | 1.07E-17 |
| KIRP | C2orf18 | 65% | ITM2B | 74% | 92% | 3.46E-15 |
| LIHC | AKR1C3 | 60% | EFNA1 | 65% | 83% | 6.12E-12 |
| PRAD | ERGIC1 | 79% | CREB3L1 | 67% | 91% | 4.22E-20 |
| PRAD | ERGIC1 | 79% | DNAH8 | 59% | 91% | 6.43E-31 |
| SKCM | ABL2 | 65% | HMCN1 | 58% | 83% | 3.99E-17 |
| THCA | S100A13 | 73% | SLC17A5 | 67% | 88% | 2.32E-15 |
| THCA | S100A13 | 73% | LTBP3 | 66% | 88% | 1.81E-16 |
| UCEC | DLX5 | 56% | EYA2 | 58% | 79% | 5.64E-06 |
| UCEC | DLX5 | 56% | CAPS | 58% | 79% | 5.64E-06 |
P-value denotes the significance of two-gene combination compared with the Gene 1 or Gene 2 by Chi-square test. Co-frequency denotes the frequency of high expression of one of the two genes in the cancer type.
The two-gene combinations with highest frequency as cSEG markers in 13 cancers
| Cancer . | Gene 1 . | Gene 1 frequency . | Gene 2 . | Gene 2 frequency . | Co-frequency . | P-value of two-gene combination . |
|---|---|---|---|---|---|---|
| BLCA | FER1L4 | 54% | SHISA5 | 66% | 75% | 5.07E-10 |
| BRCA | GALNT6 | 58% | GATA3 | 63% | 75% | 3.44E-17 |
| CESC | KLHDC7B | 55% | TCAM1P | 61% | 84% | 1.19E-14 |
| CHOL | ARRDC2 | 61% | ANXA9 | 64% | 81% | 0.12 |
| CHOL | ARRDC2 | 61% | GMNN | 58% | 81% | 0.07 |
| CHOL | ARRDC2 | 61% | SLFN13 | 64% | 81% | 0.12 |
| HNSC | LAMB3 | 60% | ALOXE3 | 56% | 80% | 1.10E-16 |
| HNSC | LAMB3 | 60% | TM4SF19 | 56% | 80% | 1.10E-16 |
| HNSC | DNAH17 | 54% | ITGA6 | 61% | 80% | 6.16E-19 |
| KICH | ACO2 | 82% | ARSJ | 58% | 97% | 2.08E-07 |
| KICH | ACO2 | 82% | CLNK | 68% | 97% | 0.000036 |
| KICH | DLAT | 70% | OGDH | 83% | 97% | 0.000072 |
| KICH | ELOVL7 | 67% | PPDPF | 70% | 97% | 0.000018 |
| KIRC | NRP1 | 69% | FBXO17 | 70% | 89% | 1.81E-15 |
| KIRC | NRP1 | 69% | HMOX1 | 66% | 89% | 4.23E-19 |
| KIRC | NRP1 | 69% | SPAG4 | 67% | 89% | 1.05E-17 |
| KIRC | FLT1 | 63% | SPAG4 | 67% | 89% | 5.16E-23 |
| KIRP | C2orf18 | 65% | CREB5 | 62% | 92% | 1.07E-17 |
| KIRP | C2orf18 | 65% | ITM2B | 74% | 92% | 3.46E-15 |
| LIHC | AKR1C3 | 60% | EFNA1 | 65% | 83% | 6.12E-12 |
| PRAD | ERGIC1 | 79% | CREB3L1 | 67% | 91% | 4.22E-20 |
| PRAD | ERGIC1 | 79% | DNAH8 | 59% | 91% | 6.43E-31 |
| SKCM | ABL2 | 65% | HMCN1 | 58% | 83% | 3.99E-17 |
| THCA | S100A13 | 73% | SLC17A5 | 67% | 88% | 2.32E-15 |
| THCA | S100A13 | 73% | LTBP3 | 66% | 88% | 1.81E-16 |
| UCEC | DLX5 | 56% | EYA2 | 58% | 79% | 5.64E-06 |
| UCEC | DLX5 | 56% | CAPS | 58% | 79% | 5.64E-06 |
| Cancer . | Gene 1 . | Gene 1 frequency . | Gene 2 . | Gene 2 frequency . | Co-frequency . | P-value of two-gene combination . |
|---|---|---|---|---|---|---|
| BLCA | FER1L4 | 54% | SHISA5 | 66% | 75% | 5.07E-10 |
| BRCA | GALNT6 | 58% | GATA3 | 63% | 75% | 3.44E-17 |
| CESC | KLHDC7B | 55% | TCAM1P | 61% | 84% | 1.19E-14 |
| CHOL | ARRDC2 | 61% | ANXA9 | 64% | 81% | 0.12 |
| CHOL | ARRDC2 | 61% | GMNN | 58% | 81% | 0.07 |
| CHOL | ARRDC2 | 61% | SLFN13 | 64% | 81% | 0.12 |
| HNSC | LAMB3 | 60% | ALOXE3 | 56% | 80% | 1.10E-16 |
| HNSC | LAMB3 | 60% | TM4SF19 | 56% | 80% | 1.10E-16 |
| HNSC | DNAH17 | 54% | ITGA6 | 61% | 80% | 6.16E-19 |
| KICH | ACO2 | 82% | ARSJ | 58% | 97% | 2.08E-07 |
| KICH | ACO2 | 82% | CLNK | 68% | 97% | 0.000036 |
| KICH | DLAT | 70% | OGDH | 83% | 97% | 0.000072 |
| KICH | ELOVL7 | 67% | PPDPF | 70% | 97% | 0.000018 |
| KIRC | NRP1 | 69% | FBXO17 | 70% | 89% | 1.81E-15 |
| KIRC | NRP1 | 69% | HMOX1 | 66% | 89% | 4.23E-19 |
| KIRC | NRP1 | 69% | SPAG4 | 67% | 89% | 1.05E-17 |
| KIRC | FLT1 | 63% | SPAG4 | 67% | 89% | 5.16E-23 |
| KIRP | C2orf18 | 65% | CREB5 | 62% | 92% | 1.07E-17 |
| KIRP | C2orf18 | 65% | ITM2B | 74% | 92% | 3.46E-15 |
| LIHC | AKR1C3 | 60% | EFNA1 | 65% | 83% | 6.12E-12 |
| PRAD | ERGIC1 | 79% | CREB3L1 | 67% | 91% | 4.22E-20 |
| PRAD | ERGIC1 | 79% | DNAH8 | 59% | 91% | 6.43E-31 |
| SKCM | ABL2 | 65% | HMCN1 | 58% | 83% | 3.99E-17 |
| THCA | S100A13 | 73% | SLC17A5 | 67% | 88% | 2.32E-15 |
| THCA | S100A13 | 73% | LTBP3 | 66% | 88% | 1.81E-16 |
| UCEC | DLX5 | 56% | EYA2 | 58% | 79% | 5.64E-06 |
| UCEC | DLX5 | 56% | CAPS | 58% | 79% | 5.64E-06 |
P-value denotes the significance of two-gene combination compared with the Gene 1 or Gene 2 by Chi-square test. Co-frequency denotes the frequency of high expression of one of the two genes in the cancer type.
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