This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 17334 genes and 9 clinical features across 263 samples, statistically thresholded by Q value < 0.05, 8 clinical features related to at least one genes.
-
303 genes correlated to 'Time to Death'.
-
FLJ42289 , PPP3CB , TLL2 , RPRD2 , RIOK3 , ...
-
17 genes correlated to 'AGE'.
-
ELOVL2 , MRPS33 , UNC80 , DOK6 , TSPYL5 , ...
-
75 genes correlated to 'GENDER'.
-
UTP14C , KIF4B , CCDC146 , CAV2 , C5ORF27 , ...
-
592 genes correlated to 'PATHOLOGY.T'.
-
KDR , DBX2 , ACTA1 , OPRK1 , NR5A1 , ...
-
7 genes correlated to 'PATHOLOGY.N'.
-
CARD16 , CASP1 , SFXN5 , ZFP64 , VGF , ...
-
49 genes correlated to 'PATHOLOGICSPREAD(M)'.
-
C20ORF112 , OPRK1 , HTR6 , PLCD1 , SESN1 , ...
-
624 genes correlated to 'TUMOR.STAGE'.
-
KDR , ACTA1 , OPRK1 , DBX2 , MYO10 , ...
-
133 genes correlated to 'NEOADJUVANT.THERAPY'.
-
CRYAA , ALDOB , NKIRAS2 , PLXNB2 , MREG , ...
-
No genes correlated to 'KARNOFSKY.PERFORMANCE.SCORE'
Complete statistical result table is provided in Supplement Table 1
Table 1. Get Full Table This table shows the clinical features, statistical methods used, and the number of genes that are significantly associated with each clinical feature at Q value < 0.05.
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=303 | shorter survival | N=185 | longer survival | N=118 |
AGE | Spearman correlation test | N=17 | older | N=14 | younger | N=3 |
GENDER | t test | N=75 | male | N=7 | female | N=68 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
PATHOLOGY T | Spearman correlation test | N=592 | higher pT | N=306 | lower pT | N=286 |
PATHOLOGY N | t test | N=7 | n1 | N=0 | n0 | N=7 |
PATHOLOGICSPREAD(M) | t test | N=49 | m1 | N=46 | m0 | N=3 |
TUMOR STAGE | Spearman correlation test | N=624 | higher stage | N=419 | lower stage | N=205 |
NEOADJUVANT THERAPY | t test | N=133 | yes | N=52 | no | N=81 |
Table S1. Basic characteristics of clinical feature: 'Time to Death'
Time to Death | Duration (Months) | 0.1-109.9 (median=28.3) |
censored | N = 169 | |
death | N = 91 | |
Significant markers | N = 303 | |
associated with shorter survival | 185 | |
associated with longer survival | 118 |
Table S2. Get Full Table List of top 10 genes significantly associated with 'Time to Death' by Cox regression test
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
FLJ42289 | 0.03 | 1.298e-11 | 2.3e-07 | 0.309 |
PPP3CB | 0 | 2.657e-11 | 4.6e-07 | 0.332 |
TLL2 | 0.02 | 2.802e-11 | 4.9e-07 | 0.322 |
RPRD2 | 50 | 7.839e-11 | 1.4e-06 | 0.676 |
RIOK3 | 6001 | 1.019e-10 | 1.8e-06 | 0.661 |
ARHGEF12 | 38 | 2.288e-10 | 4e-06 | 0.64 |
IGLL1 | 0.01 | 4.758e-10 | 8.2e-06 | 0.315 |
MBNL2 | 26 | 5.475e-10 | 9.5e-06 | 0.666 |
EVI2A | 0.04 | 5.908e-10 | 1e-05 | 0.352 |
CCL26 | 0.07 | 6e-10 | 1e-05 | 0.358 |
Figure S1. Get High-res Image As an example, this figure shows the association of FLJ42289 to 'Time to Death'. four curves present the cumulative survival rates of 4 quartile subsets of patients. P value = 1.3e-11 with univariate Cox regression analysis using continuous log-2 expression values.
![](V1ex.png)
Table S3. Basic characteristics of clinical feature: 'AGE'
AGE | Mean (SD) | 61.45 (12) |
Significant markers | N = 17 | |
pos. correlated | 14 | |
neg. correlated | 3 |
Table S4. Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
ELOVL2 | 0.4639 | 1.942e-15 | 3.37e-11 |
MRPS33 | 0.3348 | 2.626e-08 | 0.000455 |
UNC80 | 0.3241 | 7.597e-08 | 0.00132 |
DOK6 | 0.3232 | 8.284e-08 | 0.00144 |
TSPYL5 | 0.3108 | 2.681e-07 | 0.00465 |
RANBP17 | 0.3102 | 2.837e-07 | 0.00492 |
ME3 | -0.3066 | 3.965e-07 | 0.00687 |
ZYG11A | 0.3056 | 4.319e-07 | 0.00748 |
C7ORF13 | 0.3039 | 5.048e-07 | 0.00875 |
RNF32 | 0.3039 | 5.048e-07 | 0.00875 |
Figure S2. Get High-res Image As an example, this figure shows the association of ELOVL2 to 'AGE'. P value = 1.94e-15 with Spearman correlation analysis. The straight line presents the best linear regression.
![](V2ex.png)
Table S5. Basic characteristics of clinical feature: 'GENDER'
GENDER | Labels | N |
FEMALE | 89 | |
MALE | 174 | |
Significant markers | N = 75 | |
Higher in MALE | 7 | |
Higher in FEMALE | 68 |
Table S6. Get Full Table List of top 10 genes differentially expressed by 'GENDER'
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
UTP14C | 17.16 | 3.173e-32 | 5.5e-28 | 0.9707 |
KIF4B | -11.32 | 3.408e-23 | 5.91e-19 | 0.875 |
CCDC146 | -10.37 | 3.088e-21 | 5.35e-17 | 0.8014 |
CAV2 | -9.9 | 2.448e-19 | 4.24e-15 | 0.8063 |
C5ORF27 | -9.92 | 3.732e-19 | 6.47e-15 | 0.8123 |
UQCRH | 9.84 | 6.178e-19 | 1.07e-14 | 0.7634 |
DNAJB13 | -9.53 | 1.652e-18 | 2.86e-14 | 0.7841 |
SNORA48 | -9.2 | 1.193e-16 | 2.07e-12 | 0.8144 |
TLE1 | -9.1 | 3.69e-16 | 6.39e-12 | 0.8029 |
ADAMTS10 | -8.1 | 2.187e-14 | 3.79e-10 | 0.733 |
Figure S3. Get High-res Image As an example, this figure shows the association of UTP14C to 'GENDER'. P value = 3.17e-32 with T-test analysis.
![](V3ex.png)
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
Table S7. Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 92.92 (8.6) |
Score | N | |
70 | 1 | |
80 | 3 | |
90 | 8 | |
100 | 12 | |
Significant markers | N = 0 |
Table S8. Basic characteristics of clinical feature: 'PATHOLOGY.T'
PATHOLOGY.T | Mean (SD) | 1.99 (0.99) |
N | ||
T1 | 121 | |
T2 | 32 | |
T3 | 102 | |
T4 | 8 | |
Significant markers | N = 592 | |
pos. correlated | 306 | |
neg. correlated | 286 |
Table S9. Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
KDR | 0.4995 | 5.251e-18 | 9.1e-14 |
DBX2 | 0.4605 | 3.275e-15 | 5.68e-11 |
ACTA1 | 0.456 | 6.593e-15 | 1.14e-10 |
OPRK1 | 0.452 | 1.196e-14 | 2.07e-10 |
NR5A1 | 0.436 | 1.251e-13 | 2.17e-09 |
SLC35F1 | 0.4346 | 1.528e-13 | 2.65e-09 |
AVPR1A | 0.4299 | 2.97e-13 | 5.15e-09 |
RRM2 | -0.4298 | 3.015e-13 | 5.22e-09 |
MSX2P1 | 0.422 | 8.81e-13 | 1.53e-08 |
FAM38B | 0.4207 | 1.047e-12 | 1.81e-08 |
Figure S4. Get High-res Image As an example, this figure shows the association of KDR to 'PATHOLOGY.T'. P value = 5.25e-18 with Spearman correlation analysis.
![](V5ex.png)
Table S10. Basic characteristics of clinical feature: 'PATHOLOGY.N'
PATHOLOGY.N | Labels | N |
N0 | 118 | |
N1 | 9 | |
Significant markers | N = 7 | |
Higher in N1 | 0 | |
Higher in N0 | 7 |
Table S11. Get Full Table List of 7 genes differentially expressed by 'PATHOLOGY.N'
T(pos if higher in 'N1') | ttestP | Q | AUC | |
---|---|---|---|---|
CARD16 | -6.25 | 1.428e-08 | 0.000248 | 0.6638 |
CASP1 | -6.25 | 1.428e-08 | 0.000248 | 0.6638 |
SFXN5 | -6.21 | 3.299e-07 | 0.00572 | 0.7109 |
ZFP64 | -5.31 | 5.358e-07 | 0.00929 | 0.6252 |
VGF | -5.16 | 9.519e-07 | 0.0165 | 0.6544 |
SYNCRIP | -5.02 | 2.001e-06 | 0.0347 | 0.7354 |
PLAG1 | -4.91 | 2.814e-06 | 0.0488 | 0.7702 |
Figure S5. Get High-res Image As an example, this figure shows the association of CARD16 to 'PATHOLOGY.N'. P value = 1.43e-08 with T-test analysis.
![](V6ex.png)
Table S12. Basic characteristics of clinical feature: 'PATHOLOGICSPREAD(M)'
PATHOLOGICSPREAD(M) | Labels | N |
M0 | 213 | |
M1 | 50 | |
Significant markers | N = 49 | |
Higher in M1 | 46 | |
Higher in M0 | 3 |
Table S13. Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGICSPREAD(M)'
T(pos if higher in 'M1') | ttestP | Q | AUC | |
---|---|---|---|---|
C20ORF112 | 7.2 | 2.774e-11 | 4.81e-07 | 0.7599 |
OPRK1 | 7.21 | 1.558e-10 | 2.7e-06 | 0.7607 |
HTR6 | 6.94 | 8.291e-10 | 1.44e-05 | 0.7642 |
PLCD1 | 6.33 | 1.963e-09 | 3.4e-05 | 0.7057 |
SESN1 | 6.03 | 1.465e-08 | 0.000254 | 0.7013 |
GFPT1 | 5.96 | 2.322e-08 | 0.000402 | 0.6902 |
MUSK | 5.95 | 2.423e-08 | 0.00042 | 0.7065 |
STK24 | 6.09 | 2.51e-08 | 0.000435 | 0.7486 |
ASB4 | 5.98 | 3.053e-08 | 0.000529 | 0.7233 |
NBLA00301 | 6.03 | 3.129e-08 | 0.000542 | 0.713 |
Figure S6. Get High-res Image As an example, this figure shows the association of C20ORF112 to 'PATHOLOGICSPREAD(M)'. P value = 2.77e-11 with T-test analysis.
![](V7ex.png)
Table S14. Basic characteristics of clinical feature: 'TUMOR.STAGE'
TUMOR.STAGE | Mean (SD) | 2.22 (1.2) |
N | ||
Stage 1 | 119 | |
Stage 2 | 21 | |
Stage 3 | 68 | |
Stage 4 | 55 | |
Significant markers | N = 624 | |
pos. correlated | 419 | |
neg. correlated | 205 |
Table S15. Get Full Table List of top 10 genes significantly correlated to 'TUMOR.STAGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
KDR | 0.5203 | 1.214e-19 | 2.1e-15 |
ACTA1 | 0.4863 | 5.134e-17 | 8.9e-13 |
OPRK1 | 0.4738 | 3.991e-16 | 6.92e-12 |
DBX2 | 0.4657 | 1.47e-15 | 2.55e-11 |
MYO10 | 0.4645 | 1.769e-15 | 3.07e-11 |
FAM38B | 0.4601 | 3.481e-15 | 6.03e-11 |
NR5A1 | 0.4537 | 9.253e-15 | 1.6e-10 |
DLL3 | 0.4516 | 1.267e-14 | 2.19e-10 |
AVPR1A | 0.4515 | 1.287e-14 | 2.23e-10 |
NEUROD2 | 0.4464 | 2.764e-14 | 4.79e-10 |
Figure S7. Get High-res Image As an example, this figure shows the association of KDR to 'TUMOR.STAGE'. P value = 1.21e-19 with Spearman correlation analysis.
![](V8ex.png)
Table S16. Basic characteristics of clinical feature: 'NEOADJUVANT.THERAPY'
NEOADJUVANT.THERAPY | Labels | N |
NO | 4 | |
YES | 259 | |
Significant markers | N = 133 | |
Higher in YES | 52 | |
Higher in NO | 81 |
Table S17. Get Full Table List of top 10 genes differentially expressed by 'NEOADJUVANT.THERAPY'
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
CRYAA | -11.47 | 9.127e-25 | 1.58e-20 | 0.7857 |
ALDOB | -12.78 | 1.119e-24 | 1.94e-20 | 0.8243 |
NKIRAS2 | 12.69 | 2.189e-23 | 3.79e-19 | 0.8909 |
PLXNB2 | 11.55 | 6.458e-22 | 1.12e-17 | 0.7761 |
MREG | 11.5 | 6.338e-20 | 1.1e-15 | 0.7597 |
UQCRH | 9.8 | 1.679e-19 | 2.91e-15 | 0.6467 |
RDX | 20.73 | 8.317e-19 | 1.44e-14 | 0.9479 |
METTL3 | -17.65 | 1.49e-18 | 2.58e-14 | 0.8983 |
KIAA0114 | 8.87 | 5.748e-16 | 9.95e-12 | 0.7191 |
GRIN1 | -10.33 | 6.6e-16 | 1.14e-11 | 0.8485 |
Figure S8. Get High-res Image As an example, this figure shows the association of CRYAA to 'NEOADJUVANT.THERAPY'. P value = 9.13e-25 with T-test analysis.
![](V9ex.png)
-
Expresson data file = KIRC.meth.for_correlation.filtered_data.txt
-
Clinical data file = KIRC.clin.merged.picked.txt
-
Number of patients = 263
-
Number of genes = 17334
-
Number of clinical features = 9
For survival clinical features, Wald's test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values using the 'coxph' function in R. Kaplan-Meier survival curves were plot using the four quartile subgroups of patients based on expression levels
For continuous numerical clinical features, Spearman's rank correlation coefficients (Spearman 1904) and two-tailed P values were estimated using 'cor.test' function in R
For two-class clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2-expression levels between the two clinical classes using 't.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.