Table 2.
Models generated by the CoxBoost approach; model 1 includes microarray data only (29 transcripts), whereas model 2 includes microarray data (23 transcripts) as well as age, histology at baseline, deltaNp63, and podoplanin expression at baseline (clinical and pathological covariates were mandatory); P-values and hazard ratio (HR) are from the single-variate Cox model. The CoxBoost procedure was repeated 100 times, each time yielding a different set of predictive marker genes. The column “Frequency” showed the frequency of occurrences of the genes.
| Model 1 includes 29 transcripts | |||||
|---|---|---|---|---|---|
| Probeset ID | Gene symbol§ | CoxBoost coefficient | Frequency | Cox p-value | Cox hazard ratio |
| 8095441 | CSN1S2A | 0.22 | 100% | 1.80E-06 | 160.02 |
| 8023314 | CCDC11 | 0.19 | 100% | 1.80E-06 | 3.20 |
| 7986442 | ENST00000391004 | 0.13 | 100% | 3.40E-07 | 14.70 |
| 8062842 | ENST00000387867 | 0.10 | 100% | 2.50E-06 | 101.75 |
| 8084002 | KCNMB2 | 0.08 | 99% | 6.60E-05 | 5.76 |
| 7915846 | MKNK1 | 0.06 | 100% | 2.50E-08 | 39.03 |
| 8165709 | NC_001807 | 0.05 | 99% | 6.80E-05 | 9.71 |
| 8122200 | ENST00000385892 | 0.05 | 79% | 2.10E-04 | 3.82 |
| 8046408 | PDK1 | 0.04 | 93% | 3.00E-03 | 5.41 |
| 8153223 | PTK2 | 0.04 | 90% | 1.30E-03 | 6.40 |
| 8172119 | MED14 | 0.03 | 98% | 2.30E-06 | 26.81 |
| 8061092 | NA | 0.02 | 96% | 4.00E-04 | 8.35 |
| 7927106 | ENST00000387096 | 0.02 | 85% | 8.50E-07 | 3.90 |
| 7948894 | RNU2-1 | 0.02 | 59% | 8.50E-04 | 3.93 |
| 8083939 | AK128090 | −0.02 | 20% | 1.10E-01 | 0.19 |
| 7939865 | OR4B1 | −0.02 | 37% | 4.00E-03 | 0.08 |
| 7916777 | hsa-mir-101-1 | −0.02 | 51% | 1.00E-05 | 0.01 |
| 7964360 | STAT6 | −0.02 | 72% | 3.70E-05 | 0.01 |
| 8101762 | SNCA | −0.02 | 75% | 2.20E-03 | 0.39 |
| 7962489 | PLEKHA9 | −0.03 | 99% | 9.80E-05 | 0.07 |
| 7901361 | ENST00000387793 | −0.04 | 86% | 5.50E-04 | 0.12 |
| 8044682 | SNRPA1 | −0.04 | 96% | 1.40E-02 | 0.18 |
| 8028950 | CYP2G1P | −0.04 | 69% | 1.70E-02 | 0.06 |
| 7977480 | ENST00000386651 | −0.04 | 95% | 7.00E-05 | 0.04 |
| 8067983 | ENST00000387011 | −0.08 | 100% | 7.50E-05 | 0.01 |
| 8097743 | ENST00000410285 | −0.10 | 100% | 9.90E-06 | 0.07 |
| 8093957 | CNO | −0.12 | 100% | 6.50E-07 | 0.02 |
| 8086536 | ENST00000365398 | −0.15 | 100% | 2.00E-05 | 0.02 |
| 8121943 | ENST00000384255 | −0.18 | 100% | 8.90E-05 | 0.03 |
| Model 2 includes 23 transcripts and age, histology at baseline, podoplanin and deltaNp63 expression at baseline | |||||
|---|---|---|---|---|---|
| Probeset_ID | Gene symbol§ | CoxBoost coefficient | Frequency | Cox p-value | Cox hazard ratio |
| 8061746 | DNMT3B | 0.26 | 100% | 4.30E-06 | 7.73 |
| 8092638 | ENST00000384774 | 0.21 | 100% | 2.40E-10 | 18.56 |
| 8165709 | NC_001807 | 0.19 | 100% | 6.80E-05 | 9.71 |
| 7949019 | ENST00000365219 | 0.14 | 100% | 4.40E-08 | 9.30 |
| 7978905 | SDCCAG1 | 0.13 | 100% | 4.20E-09 | 79.79 |
| 7959891 | ENST00000384123 | 0.09 | 91% | 3.20E-05 | 10.63 |
| 8023314 | CCDC11 | 0.09 | 95% | 1.80E-06 | 3.20 |
| 7907769 | FAM163A | 0.07 | 98% | 1.50E-03 | 18.37 |
| 8095441 | CSN1S2A | 0.06 | 98% | 1.80E-06 | 160.02 |
| 8175119 | ENST00000410882 | 0.05 | 40% | 1.00E-02 | 9.54 |
| 7918757 | DENND2C | 0.03 | 22% | 4.20E-05 | 6.62 |
| 8063839 | SS18L1 | 0.03 | 23% | 8.50E-04 | 30.51 |
| 8078600 | TCEA1 | 0.02 | 20% | 2.40E-04 | 11.92 |
| 8046408 | PDK1 | 0.02 | 12% | 3.00E-03 | 5.41 |
| 7925939 | AKR1C4 | 0.02 | 10% | 3.60E-04 | 4.35 |
| 8134599 | CPSF4 | −0.02 | 4% | 1.50E-03 | 0.06 |
| 7964183 | GLS2 | −0.02 | 54% | 3.50E-04 | 0.04 |
| 7901361 | ENST00000387793 | −0.08 | 98% | 5.50E-04 | 0.12 |
| 8121943 | ENST00000384255 | −0.12 | 99% | 8.90E-05 | 0.03 |
| 7916777 | hsa-mir-101-1 | −0.15 | 100% | 1.00E-05 | 0.01 |
| 8045339 | ENST00000363848 | −0.15 | 100% | 7.00E-07 | 0.10 |
| 8067983 | ENST00000387011 | −0.19 | 100% | 7.50E-05 | 0.01 |
| 8093957 | CNO | −0.26 | 100% | 6.50E-07 | 0.02 |
| Clinical and Pathological covariates | CoxBoost coefficient | Frequency | Cox p-value | Cox hazard ratio | |
|---|---|---|---|---|---|
| Age | 0.012 | 100% | 7.60E-02 | 1.03 | |
| Histology at baseline | 0.078 | 100% | 2.00E-01 | 0.64 | |
| Podoplanin | 0.43 | 100% | 3.30E-03 | 3.10 | |
| DeltaNp63 | 1.47 | 100% | 5.69E-05 | 4.31 | |