(Regional_Metastatic cohort)
This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 17159 genes and 7 clinical features across 142 samples, statistically thresholded by Q value < 0.05, 7 clinical features related to at least one genes.
-
1 gene correlated to 'Time to Death'.
-
NR4A3
-
13 genes correlated to 'AGE'.
-
NUP155 , NIPAL2 , ITGA8 , HAPLN1 , STBD1 , ...
-
95 genes correlated to 'PRIMARY.SITE.OF.DISEASE'.
-
NT5M , IGSF6 , CLECL1 , LTA , ANKRD13A , ...
-
1 gene correlated to 'GENDER'.
-
UTP14C
-
309 genes correlated to 'DISTANT.METASTASIS'.
-
CCNG1 , IFT57 , FAM65C , LMF1 , POLE4 , ...
-
43 genes correlated to 'LYMPH.NODE.METASTASIS'.
-
CCDC25 , KIF20A , NGLY1 , MBIP , TMEM184B , ...
-
10 genes correlated to 'NEOPLASM.DISEASESTAGE'.
-
UBE2I , PIM3 , FUT11 , RAB11FIP4 , ELP2 , ...
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=1 | shorter survival | N=0 | longer survival | N=1 |
AGE | Spearman correlation test | N=13 | older | N=13 | younger | N=0 |
PRIMARY SITE OF DISEASE | t test | N=95 | regional lymph node | N=33 | regional cutaneous or subcutaneous tissue (includes satellite and in-transit metastasis) | N=62 |
GENDER | t test | N=1 | male | N=1 | female | N=0 |
DISTANT METASTASIS | ANOVA test | N=309 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=43 | ||||
NEOPLASM DISEASESTAGE | ANOVA test | N=10 |
Time to Death | Duration (Months) | 2.6-346 (median=47.5) |
censored | N = 74 | |
death | N = 66 | |
Significant markers | N = 1 | |
associated with shorter survival | 0 | |
associated with longer survival | 1 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
NR4A3 | 0.05 | 1.231e-06 | 0.021 | 0.319 |
AGE | Mean (SD) | 55.8 (16) |
Significant markers | N = 13 | |
pos. correlated | 13 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
NUP155 | 0.4438 | 3.169e-08 | 0.000544 |
NIPAL2 | 0.4291 | 9.914e-08 | 0.0017 |
ITGA8 | 0.4084 | 4.512e-07 | 0.00774 |
HAPLN1 | 0.3992 | 8.589e-07 | 0.0147 |
STBD1 | 0.3945 | 1.182e-06 | 0.0203 |
FAS | 0.3935 | 1.272e-06 | 0.0218 |
TRPV4 | 0.392 | 1.404e-06 | 0.0241 |
POSTN | 0.3895 | 1.663e-06 | 0.0285 |
BBX | 0.3894 | 1.673e-06 | 0.0287 |
PTX3 | 0.3864 | 2.034e-06 | 0.0349 |
PRIMARY.SITE.OF.DISEASE | Labels | N |
REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | 32 | |
REGIONAL LYMPH NODE | 110 | |
Significant markers | N = 95 | |
Higher in REGIONAL LYMPH NODE | 33 | |
Higher in REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | 62 |
T(pos if higher in 'REGIONAL LYMPH NODE') | ttestP | Q | AUC | |
---|---|---|---|---|
NT5M | 7.59 | 4.503e-12 | 7.73e-08 | 0.7778 |
IGSF6 | -7.13 | 4.971e-11 | 8.53e-07 | 0.7557 |
CLECL1 | -6.58 | 8.669e-10 | 1.49e-05 | 0.719 |
LTA | -6.56 | 9.814e-10 | 1.68e-05 | 0.7426 |
ANKRD13A | -6.54 | 1.224e-09 | 2.1e-05 | 0.733 |
ISCU | -6.63 | 1.345e-09 | 2.31e-05 | 0.7534 |
DCLRE1C | -6.43 | 1.971e-09 | 3.38e-05 | 0.7384 |
IL4I1 | -6.31 | 3.794e-09 | 6.51e-05 | 0.7347 |
ABTB1 | -6.35 | 3.847e-09 | 6.6e-05 | 0.7739 |
TAP1 | -6.29 | 9.945e-09 | 0.000171 | 0.7611 |
GENDER | Labels | N |
FEMALE | 50 | |
MALE | 92 | |
Significant markers | N = 1 | |
Higher in MALE | 1 | |
Higher in FEMALE | 0 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
UTP14C | 10.06 | 3.89e-14 | 6.67e-10 | 0.9387 |
DISTANT.METASTASIS | Labels | N |
M0 | 123 | |
M1 | 1 | |
M1A | 2 | |
M1B | 2 | |
M1C | 1 | |
Significant markers | N = 309 |
ANOVA_P | Q | |
---|---|---|
CCNG1 | 6.583e-116 | 1.13e-111 |
IFT57 | 9.002e-21 | 1.54e-16 |
FAM65C | 2.861e-20 | 4.91e-16 |
LMF1 | 1.076e-17 | 1.85e-13 |
POLE4 | 1.463e-17 | 2.51e-13 |
CASC5 | 3.479e-17 | 5.97e-13 |
COL5A1 | 3.599e-17 | 6.17e-13 |
C10ORF88 | 4.154e-16 | 7.12e-12 |
PXK | 4.773e-16 | 8.19e-12 |
MAN2A1 | 5.262e-16 | 9.02e-12 |
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 76 | |
N1 | 2 | |
N1A | 5 | |
N1B | 11 | |
N2 | 1 | |
N2A | 4 | |
N2B | 10 | |
N2C | 4 | |
N3 | 15 | |
NX | 2 | |
Significant markers | N = 43 |
ANOVA_P | Q | |
---|---|---|
CCDC25 | 3.889e-140 | 6.67e-136 |
KIF20A | 3.319e-67 | 5.69e-63 |
NGLY1 | 4.605e-59 | 7.9e-55 |
MBIP | 2.013e-56 | 3.45e-52 |
TMEM184B | 2.829e-35 | 4.85e-31 |
C6ORF162 | 1.001e-33 | 1.72e-29 |
C17ORF63 | 2.596e-24 | 4.45e-20 |
ASAP3 | 6.556e-20 | 1.12e-15 |
NOS1 | 1.416e-18 | 2.43e-14 |
CSRP2BP | 2.935e-18 | 5.03e-14 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 16 | |
STAGE IA | 8 | |
STAGE IB | 13 | |
STAGE II | 17 | |
STAGE IIA | 7 | |
STAGE IIB | 8 | |
STAGE IIC | 4 | |
STAGE III | 7 | |
STAGE IIIA | 4 | |
STAGE IIIB | 15 | |
STAGE IIIC | 20 | |
STAGE IV | 4 | |
Significant markers | N = 10 |
-
Expresson data file = SKCM-Regional_Metastatic.meth.for_correlation.filtered_data.txt
-
Clinical data file = SKCM-Regional_Metastatic.clin.merged.picked.txt
-
Number of patients = 142
-
Number of genes = 17159
-
Number of clinical features = 7
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 multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' 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.