Correlation between gene methylation status and clinical features
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene methylation status and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1BK1B3W
Overview
Introduction

This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.

Summary

Testing the association between 20185 genes and 13 clinical features across 423 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 9 clinical features related to at least one genes.

  • 7 genes correlated to 'AGE'.

    • KIAA1143 ,  KIF15 ,  CHMP6 ,  ACN9 ,  TRIM45 ,  ...

  • 5 genes correlated to 'PATHOLOGY.T.STAGE'.

    • STAT3 ,  LOC729121 ,  RGPD4 ,  MAP4K4 ,  UPP1

  • 7 genes correlated to 'PATHOLOGY.N.STAGE'.

    • EFEMP1 ,  SLC47A2 ,  DSG1 ,  FAM185A ,  AVPI1 ,  ...

  • 136 genes correlated to 'PATHOLOGY.M.STAGE'.

    • CCDC102B ,  TMX3 ,  METTL3 ,  C19ORF2 ,  WDR54 ,  ...

  • 93 genes correlated to 'GENDER'.

    • KIF4B ,  FRG1B ,  MRPL32 ,  PSMA2__1 ,  NCRNA00116 ,  ...

  • 699 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

    • HSPB1 ,  SNRNP40 ,  ZCCHC17 ,  NFS1 ,  ROMO1 ,  ...

  • 44 genes correlated to 'NUMBERPACKYEARSSMOKED'.

    • KLF6 ,  ELL ,  SCN9A ,  DBF4__1 ,  LRIG1 ,  ...

  • 39 genes correlated to 'NUMBER.OF.LYMPH.NODES'.

    • FAM185A ,  HSPB3 ,  P2RY6 ,  AVPI1 ,  ISLR2 ,  ...

  • 6 genes correlated to 'RACE'.

    • GPBAR1 ,  EIF3D ,  HEBP2 ,  RASIP1 ,  ATAD3A ,  ...

  • No genes correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', 'HISTOLOGICAL.TYPE', and 'ETHNICITY'.

Results
Overview of the results

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 P value < 0.05 and Q value < 0.3.

Clinical feature Statistical test Significant genes Associated with                 Associated with
Time to Death Cox regression test   N=0        
AGE Spearman correlation test N=7 older N=6 younger N=1
NEOPLASM DISEASESTAGE Kruskal-Wallis test   N=0        
PATHOLOGY T STAGE Spearman correlation test N=5 higher stage N=1 lower stage N=4
PATHOLOGY N STAGE Spearman correlation test N=7 higher stage N=7 lower stage N=0
PATHOLOGY M STAGE Wilcoxon test N=136 mx N=136 m0 N=0
GENDER Wilcoxon test N=93 male N=93 female N=0
HISTOLOGICAL TYPE Kruskal-Wallis test   N=0        
RADIATIONS RADIATION REGIMENINDICATION Wilcoxon test N=699 yes N=699 no N=0
NUMBERPACKYEARSSMOKED Spearman correlation test N=44 higher numberpackyearssmoked N=6 lower numberpackyearssmoked N=38
NUMBER OF LYMPH NODES Spearman correlation test N=39 higher number.of.lymph.nodes N=39 lower number.of.lymph.nodes N=0
RACE Kruskal-Wallis test N=6        
ETHNICITY Wilcoxon test   N=0        
Clinical variable #1: 'Time to Death'

No gene related to 'Time to Death'.

Table S1.  Basic characteristics of clinical feature: 'Time to Death'

Time to Death Duration (Years) 2-3837 (median=630)
  censored N = 260
  death N = 101
     
  Significant markers N = 0
Clinical variable #2: 'AGE'

7 genes related to 'AGE'.

Table S2.  Basic characteristics of clinical feature: 'AGE'

AGE Mean (SD) 60.92 (12)
  Significant markers N = 7
  pos. correlated 6
  neg. correlated 1
List of 7 genes differentially expressed by 'AGE'

Table S3.  Get Full Table List of 7 genes significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
KIAA1143 0.2896 1.341e-09 2.71e-05
KIF15 0.2896 1.341e-09 2.71e-05
CHMP6 -0.2276 2.324e-06 0.0469
ACN9 0.2211 4.551e-06 0.0918
TRIM45 0.2146 8.67e-06 0.175
DKFZP686O24166 0.2117 1.152e-05 0.232
NAPEPLD 0.2093 1.455e-05 0.294
Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

No gene related to 'NEOPLASM.DISEASESTAGE'.

Table S4.  Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 24
  STAGE II 64
  STAGE III 71
  STAGE IVA 197
  STAGE IVB 9
     
  Significant markers N = 0
Clinical variable #4: 'PATHOLOGY.T.STAGE'

5 genes related to 'PATHOLOGY.T.STAGE'.

Table S5.  Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE Mean (SD) 2.84 (1)
  N
  1 40
  2 111
  3 86
  4 133
     
  Significant markers N = 5
  pos. correlated 1
  neg. correlated 4
List of 5 genes differentially expressed by 'PATHOLOGY.T.STAGE'

Table S6.  Get Full Table List of 5 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
STAT3 0.2393 3.248e-06 0.0656
LOC729121 -0.2387 3.436e-06 0.0693
RGPD4 -0.2387 3.436e-06 0.0693
MAP4K4 -0.2284 9.078e-06 0.183
UPP1 -0.2245 1.303e-05 0.263
Clinical variable #5: 'PATHOLOGY.N.STAGE'

7 genes related to 'PATHOLOGY.N.STAGE'.

Table S7.  Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'

PATHOLOGY.N.STAGE Mean (SD) 1.03 (0.95)
  N
  0 137
  1 56
  2 133
  3 7
     
  Significant markers N = 7
  pos. correlated 7
  neg. correlated 0
List of 7 genes differentially expressed by 'PATHOLOGY.N.STAGE'

Table S8.  Get Full Table List of 7 genes significantly correlated to 'PATHOLOGY.N.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
EFEMP1 0.2668 7.809e-07 0.0158
SLC47A2 0.2584 1.761e-06 0.0355
DSG1 0.2525 3.071e-06 0.062
FAM185A 0.2519 3.24e-06 0.0654
AVPI1 0.2456 5.788e-06 0.117
SLC43A3 0.241 8.719e-06 0.176
CFB 0.2378 1.155e-05 0.233
Clinical variable #6: 'PATHOLOGY.M.STAGE'

136 genes related to 'PATHOLOGY.M.STAGE'.

Table S9.  Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE Labels N
  M0 109
  MX 48
     
  Significant markers N = 136
  Higher in MX 136
  Higher in M0 0
List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

Table S10.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

W(pos if higher in 'MX') wilcoxontestP Q AUC
CCDC102B 4109 1.297e-08 0.000262 0.7854
TMX3 4109 1.297e-08 0.000262 0.7854
METTL3 1155 2.628e-08 0.00053 0.7792
C19ORF2 1165 3.268e-08 0.00066 0.7773
WDR54 1185 5.03e-08 0.00102 0.7735
RBPJ 4044 5.364e-08 0.00108 0.7729
SMARCA5 4008 1.148e-07 0.00232 0.7661
ABCB9 1247 1.848e-07 0.00373 0.7617
OGFOD2__1 1247 1.848e-07 0.00373 0.7617
LOC728554 1257 2.268e-07 0.00458 0.7597
Clinical variable #7: 'GENDER'

93 genes related to 'GENDER'.

Table S11.  Basic characteristics of clinical feature: 'GENDER'

GENDER Labels N
  FEMALE 123
  MALE 300
     
  Significant markers N = 93
  Higher in MALE 93
  Higher in FEMALE 0
List of top 10 genes differentially expressed by 'GENDER'

Table S12.  Get Full Table List of top 10 genes differentially expressed by 'GENDER'. 0 significant gene(s) located in sex chromosomes is(are) filtered out.

W(pos if higher in 'MALE') wilcoxontestP Q AUC
KIF4B 5623 2.802e-29 5.66e-25 0.8476
FRG1B 9128 3.253e-16 6.56e-12 0.7526
MRPL32 9790 3.356e-14 6.77e-10 0.7347
PSMA2__1 9790 3.356e-14 6.77e-10 0.7347
NCRNA00116 11203 2.205e-10 4.45e-06 0.6964
NPDC1 11303 3.881e-10 7.83e-06 0.6937
NLRP2 25447 8.933e-10 1.8e-05 0.6896
NDUFA13 11882 8.836e-09 0.000178 0.678
TSSK6 11882 8.836e-09 0.000178 0.678
TMEM232 11981 1.47e-08 0.000297 0.6753
Clinical variable #8: 'HISTOLOGICAL.TYPE'

No gene related to 'HISTOLOGICAL.TYPE'.

Table S13.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  HEAD AND NECK SQUAMOUS CELL CARCINOMA 416
  HEAD AND NECK SQUAMOUS CELL CARCINOMA SPINDLE CELL VARIANT 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE 6
     
  Significant markers N = 0
Clinical variable #9: 'RADIATIONS.RADIATION.REGIMENINDICATION'

699 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S14.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 81
  YES 342
     
  Significant markers N = 699
  Higher in YES 699
  Higher in NO 0
List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S15.  Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

W(pos if higher in 'YES') wilcoxontestP Q AUC
HSPB1 6569 1.84e-13 3.71e-09 0.7629
SNRNP40 7226 2.144e-11 4.33e-07 0.7392
ZCCHC17 7226 2.144e-11 4.33e-07 0.7392
NFS1 7244 2.428e-11 4.9e-07 0.7385
ROMO1 7244 2.428e-11 4.9e-07 0.7385
MED18 7560 2.041e-10 4.12e-06 0.7271
SFRS4 7561 2.054e-10 4.15e-06 0.7271
SNX22 7564 2.095e-10 4.23e-06 0.727
RUFY3 7602 2.688e-10 5.42e-06 0.7256
SCARNA2 7606 2.759e-10 5.57e-06 0.7254
Clinical variable #10: 'NUMBERPACKYEARSSMOKED'

44 genes related to 'NUMBERPACKYEARSSMOKED'.

Table S16.  Basic characteristics of clinical feature: 'NUMBERPACKYEARSSMOKED'

NUMBERPACKYEARSSMOKED Mean (SD) 46.6 (38)
  Significant markers N = 44
  pos. correlated 6
  neg. correlated 38
List of top 10 genes differentially expressed by 'NUMBERPACKYEARSSMOKED'

Table S17.  Get Full Table List of top 10 genes significantly correlated to 'NUMBERPACKYEARSSMOKED' by Spearman correlation test

SpearmanCorr corrP Q
KLF6 0.3438 5.265e-08 0.00106
ELL 0.3154 6.789e-07 0.0137
SCN9A -0.3101 1.066e-06 0.0215
DBF4__1 -0.3066 1.841e-06 0.0372
LRIG1 -0.3 2.448e-06 0.0494
KCNS3 -0.2974 3.006e-06 0.0607
ZMYND8__1 -0.2963 3.281e-06 0.0662
LOC648691 -0.296 3.381e-06 0.0682
PRAME -0.296 3.381e-06 0.0682
DCAF17 -0.2946 3.761e-06 0.0759
Clinical variable #11: 'NUMBER.OF.LYMPH.NODES'

39 genes related to 'NUMBER.OF.LYMPH.NODES'.

Table S18.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 2.3 (4.6)
  Significant markers N = 39
  pos. correlated 39
  neg. correlated 0
List of top 10 genes differentially expressed by 'NUMBER.OF.LYMPH.NODES'

Table S19.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
FAM185A 0.3068 1.561e-08 0.000315
HSPB3 0.2721 6.063e-07 0.0122
P2RY6 0.2682 8.898e-07 0.018
AVPI1 0.2653 1.176e-06 0.0237
ISLR2 0.2598 1.982e-06 0.04
LOC283731 0.2598 1.982e-06 0.04
ARHGAP27 0.2597 2.014e-06 0.0406
DSG1 0.2563 2.751e-06 0.0555
NBLA00301 0.2562 2.771e-06 0.0559
SLC47A2 0.2556 2.927e-06 0.0591
Clinical variable #12: 'RACE'

6 genes related to 'RACE'.

Table S20.  Basic characteristics of clinical feature: 'RACE'

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 1
  ASIAN 10
  BLACK OR AFRICAN AMERICAN 33
  WHITE 367
     
  Significant markers N = 6
List of 6 genes differentially expressed by 'RACE'

Table S21.  Get Full Table List of 6 genes differentially expressed by 'RACE'

ANOVA_P Q
GPBAR1 3.66e-09 7.39e-05
EIF3D 2.061e-06 0.0416
HEBP2 4.491e-06 0.0906
RASIP1 6.45e-06 0.13
ATAD3A 7.065e-06 0.143
C21ORF56 9.004e-06 0.182
Clinical variable #13: 'ETHNICITY'

No gene related to 'ETHNICITY'.

Table S22.  Basic characteristics of clinical feature: 'ETHNICITY'

ETHNICITY Labels N
  HISPANIC OR LATINO 18
  NOT HISPANIC OR LATINO 387
     
  Significant markers N = 0
Methods & Data
Input
  • Expresson data file = HNSC-TP.meth.by_min_clin_corr.data.txt

  • Clinical data file = HNSC-TP.merged_data.txt

  • Number of patients = 423

  • Number of genes = 20185

  • Number of clinical features = 13

Survival analysis

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

Correlation analysis

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

ANOVA analysis

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

Student's t-test analysis

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

Q value calculation

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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Andersen and Gill, Cox's regression model for counting processes, a large sample study, Annals of Statistics 10(4):1100-1120 (1982)
[2] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)
[3] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[4] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)