Table 2.
The second stage of random survival forest analysis: predictive value of variables in overall analysis
| Variable* | Minimal Depth† | VIMP | C-index | Error¶ | Drop Error§ |
|---|---|---|---|---|---|
| Duration of oral contraceptive use | 1.9450 | 0.0467 | 0.8449 | 0.1551 | 0.3449 |
| HNF4A rs1800961 | 2.5412 | 0.0263 | 0.9308 | 0.0692 | 0.0859 |
| ONECUT2 rs4092465 | 2.6928 | 0.0179 | 0.9534 | 0.0466 | 0.0226 |
| CRP rs1800947 | 2.9376 | 0.0115 | 0.9533 | 0.0467 | -0.0001 |
| METAP2 rs11108056 | 3.2086 | 0.0102 | 0.9534 | 0.0466 | 0.0001 |
| NLRP3 rs10925027 | 3.4894 | 0.0073 | 0.9554 | 0.0446 | 0.0020 |
| TOMM40 rs157581 | 3.9874 | 0.0119 | 0.9552 | 0.0448 | -0.0002 |
| TOMM40 rs157582 | 3.9934 | 0.0104 | 0.9562 | 0.0438 | 0.0011 |
| TRAIP rs2352975 | 4.2272 | 0.0027 | 0.9580 | 0.0420 | 0.0017 |
| DUSP1 rs17658229 | 4.2598 | 0.0047 | 0.9647 | 0.0353 | 0.0067 |
| TOMM40 rs11556505 | 4.3526 | 0.0123 | 0.9657 | 0.0343 | 0.0011 |
| Age at enrollment | 4.5316 | 0.0015 | 0.9654 | 0.0346 | -0.0003 |
| Waist-to-hip ratio | 5.0664 | 0.0000 | 0.9650 | 0.0350 | -0.0005 |
| RGS6 rs2239222 | 5.0824 | 0.0017 | 0.9642 | 0.0358 | -0.0007 |
| HNF1A rs11065385 | 5.0992 | 0.0041 | 0.9642 | 0.0358 | 0.0000 |
| Duration of E+P use | 5.1748 | 0.0009 | 0.9647 | 0.0353 | 0.0005 |
| Age at menopause | 5.3086 | 0.0003 | 0.9658 | 0.0342 | 0.0011 |
| HNF1A-AS1 rs2251468 | 5.3192 | 0.0057 | 0.9652 | 0.0348 | -0.0006 |
| Hip circumference | 5.3238 | -0.0001 | 0.9647 | 0.0353 | -0.0005 |
| Height | 5.4572 | -0.0001 | 0.9641 | 0.0359 | -0.0006 |
| Education | 5.5004 | -0.0002 | 0.9634 | 0.0366 | -0.0007 |
| Waist circumference | 5.5066 | -0.0002 | 0.9629 | 0.0371 | -0.0005 |
| BMI | 5.6638 | -0.0001 | 0.9627 | 0.0373 | -0.0002 |
| Total months of breastfeeding | 5.6970 | 0.0003 | 0.9621 | 0.0379 | -0.0006 |
| HNF1A-AS1 rs7953249 | 5.7660 | 0.0060 | 0.9618 | 0.0382 | -0.0004 |
| Weight | 5.8404 | -0.0001 | 0.9622 | 0.0378 | 0.0005 |
| HNF1A-AS1 rs10774579 | 6.3998 | 0.0037 | 0.9623 | 0.0377 | 0.0001 |
| HNF1A-AS1 rs1920792 | 6.4012 | 0.0037 | 0.9624 | 0.0376 | 0.0001 |
| HNF1A rs1169301 | 8.0714 | 0.0010 | 0.9617 | 0.0383 | -0.0007 |
| HNF1A rs1169300 | 8.1956 | 0.0010 | 0.9616 | 0.0384 | -0.0001 |
BMI, body mass index; C-index, concordance index; E+P, exogenous estrogen + progestin; VIMP, variable of importance.
Variables are ordered by minimal depth.
Predictive value of variable was assessed via minimal depth in the nested random survival forest models.
A lower value is likely to have a greater impact on prediction.
The incremental error rate of each variable was estimated in the nested sequence of models starting with the top variable, followed by the model with the top 2 variables, then the model with the top 3 variables, and so on.
For example, the third error rate was estimated from the third nested model (including the first, second, and third variables).
The drop error rate was estimated by the difference between the error rates from the nested models with a prior and the corresponding variable.
For example, the drop error rate of the second variable was estimated by the difference between the error rates from the first and second nested models. The error rate for the null model is set at 0.5; thus, the drop error rate for the first variable was obtained by subtracting the error rate (0.3449) from 0.5.