Correlation between gene methylation status and clinical features
Esophageal Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1736Q3K
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene methylation status and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1736Q3K
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 20580 genes and 15 clinical features across 185 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 10 clinical features related to at least one genes.

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • LYPLA2 ,  GPRC5A ,  KRBA2 ,  PTPRJ ,  CDC42EP1 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • TUSC3 ,  FAM135A ,  CLDN18 ,  BRE ,  LOC100302650 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • SSH1 ,  C9ORF167 ,  HM13__1 ,  PSIMCT-1 ,  CLDN15 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • ZNF611 ,  C8ORF58 ,  NQO1 ,  CAV3 ,  ASAP1__1 ,  ...

  • 4 genes correlated to 'GENDER'.

    • KIF4B ,  RIMBP3 ,  FAM35A ,  GLUD1

  • 30 genes correlated to 'RADIATION_THERAPY'.

    • BRE ,  LOC100302650 ,  RBKS ,  AEN ,  CCPG1 ,  ...

  • 30 genes correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

    • LOC148189 ,  C1D ,  GFM1__1 ,  NR2C1 ,  FLJ36031 ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • TMED6 ,  GLYCTK ,  RAB11FIP4 ,  DST ,  WNT4 ,  ...

  • 30 genes correlated to 'NUMBER_PACK_YEARS_SMOKED'.

    • KIAA1530 ,  TENC1 ,  D2HGDH ,  MLLT6 ,  C15ORF57 ,  ...

  • 30 genes correlated to 'RACE'.

    • GATM ,  YEATS2 ,  HABP4 ,  RIMS2 ,  DCUN1D1 ,  ...

  • No genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP', 'PATHOLOGY_M_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', 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
DAYS_TO_DEATH_OR_LAST_FUP Cox regression test   N=0        
YEARS_TO_BIRTH Spearman correlation test N=30 older N=13 younger N=17
PATHOLOGIC_STAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=27 lower stage N=3
PATHOLOGY_N_STAGE Spearman correlation test N=30 higher stage N=27 lower stage N=3
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
GENDER Wilcoxon test N=4 male N=4 female N=0
RADIATION_THERAPY Wilcoxon test N=30 yes N=30 no N=0
KARNOFSKY_PERFORMANCE_SCORE Spearman correlation test N=30 higher score N=30 lower score N=0
HISTOLOGICAL_TYPE Wilcoxon test N=30 esophagus squamous cell carcinoma N=30 esophagus adenocarcinoma nos N=0
NUMBER_PACK_YEARS_SMOKED Spearman correlation test N=30 higher number_pack_years_smoked N=2 lower number_pack_years_smoked N=28
RESIDUAL_TUMOR Kruskal-Wallis test   N=0        
NUMBER_OF_LYMPH_NODES Spearman correlation test   N=0        
RACE Kruskal-Wallis test N=30        
ETHNICITY Wilcoxon test   N=0        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

No gene related to 'DAYS_TO_DEATH_OR_LAST_FUP'.

Table S1.  Basic characteristics of clinical feature: 'DAYS_TO_DEATH_OR_LAST_FUP'

DAYS_TO_DEATH_OR_LAST_FUP Duration (Months) 0.1-122.1 (median=13.2)
  censored N = 108
  death N = 76
     
  Significant markers N = 0
Clinical variable #2: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

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

YEARS_TO_BIRTH Mean (SD) 62.46 (12)
  Significant markers N = 30
  pos. correlated 13
  neg. correlated 17
List of top 10 genes differentially expressed by 'YEARS_TO_BIRTH'

Table S3.  Get Full Table List of top 10 genes significantly correlated to 'YEARS_TO_BIRTH' by Spearman correlation test

SpearmanCorr corrP Q
LYPLA2 -0.4493 1.41e-10 2.9e-06
GPRC5A -0.404 1.182e-08 6.45e-05
KRBA2 0.402 1.415e-08 6.45e-05
PTPRJ -0.3977 2.08e-08 6.45e-05
CDC42EP1 -0.3975 2.111e-08 6.45e-05
MAP3K14 -0.3974 2.127e-08 6.45e-05
SYT14 0.3971 2.196e-08 6.45e-05
LOC148696 -0.3954 2.555e-08 6.57e-05
ARL4C 0.3928 3.183e-08 7.28e-05
LGALS9 -0.3902 3.991e-08 7.53e-05
Clinical variable #3: 'PATHOLOGIC_STAGE'

30 genes related to 'PATHOLOGIC_STAGE'.

Table S4.  Basic characteristics of clinical feature: 'PATHOLOGIC_STAGE'

PATHOLOGIC_STAGE Labels N
  STAGE I 8
  STAGE IA 5
  STAGE IB 6
  STAGE II 1
  STAGE IIA 47
  STAGE IIB 31
  STAGE III 26
  STAGE IIIA 14
  STAGE IIIB 9
  STAGE IIIC 7
  STAGE IV 5
  STAGE IVA 4
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

Table S5.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

kruskal_wallis_P Q
TUSC3 3.353e-07 0.0069
FAM135A 8.467e-07 0.00871
CLDN18 1.371e-06 0.00885
BRE 2.581e-06 0.00885
LOC100302650 2.581e-06 0.00885
RBKS 2.581e-06 0.00885
C7ORF46 4.455e-06 0.00892
DOK4 5.475e-06 0.00892
TIAM1 6.864e-06 0.00892
QRFPR 6.988e-06 0.00892
Clinical variable #4: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

Table S6.  Basic characteristics of clinical feature: 'PATHOLOGY_T_STAGE'

PATHOLOGY_T_STAGE Mean (SD) 2.39 (0.84)
  N
  T0 1
  T1 31
  T2 43
  T3 88
  T4 5
     
  Significant markers N = 30
  pos. correlated 27
  neg. correlated 3
List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S7.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
SSH1 -0.3383 7.277e-06 0.15
C9ORF167 0.3064 5.35e-05 0.229
HM13__1 0.3024 6.779e-05 0.229
PSIMCT-1 0.3024 6.779e-05 0.229
CLDN15 0.3003 7.646e-05 0.229
PKIB 0.2975 8.993e-05 0.229
MGST1 0.2928 0.0001176 0.229
C19ORF77 0.2923 0.0001206 0.229
SELV 0.2914 0.0001269 0.229
RAD18 0.2906 0.0001393 0.229
Clinical variable #5: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

Table S8.  Basic characteristics of clinical feature: 'PATHOLOGY_N_STAGE'

PATHOLOGY_N_STAGE Mean (SD) 0.7 (0.8)
  N
  N0 77
  N1 69
  N2 12
  N3 8
     
  Significant markers N = 30
  pos. correlated 27
  neg. correlated 3
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

Table S9.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_N_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
ZNF611 -0.33 1.411e-05 0.0373
C8ORF58 0.3241 2.046e-05 0.0373
NQO1 -0.319 2.8e-05 0.0373
CAV3 0.3136 3.895e-05 0.0373
ASAP1__1 0.3128 4.076e-05 0.0373
DAND5 0.3115 4.393e-05 0.0373
ZBTB17 0.3095 4.96e-05 0.0373
SUSD1 -0.3091 5.074e-05 0.0373
LOC254559 0.3082 5.342e-05 0.0373
PCDHGA1__1 0.3064 5.941e-05 0.0373
Clinical variable #6: 'PATHOLOGY_M_STAGE'

No gene related to 'PATHOLOGY_M_STAGE'.

Table S10.  Basic characteristics of clinical feature: 'PATHOLOGY_M_STAGE'

PATHOLOGY_M_STAGE Labels N
  class0 136
  class1 9
     
  Significant markers N = 0
Clinical variable #7: 'GENDER'

4 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 27
  MALE 158
     
  Significant markers N = 4
  Higher in MALE 4
  Higher in FEMALE 0
List of 4 genes differentially expressed by 'GENDER'

Table S12.  Get Full Table List of 4 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 522 3.776e-10 7.77e-06 0.8776
RIMBP3 3317 4.175e-06 0.043 0.7775
FAM35A 1079 4.187e-05 0.215 0.7471
GLUD1 1079 4.187e-05 0.215 0.7471
Clinical variable #8: 'RADIATION_THERAPY'

30 genes related to 'RADIATION_THERAPY'.

Table S13.  Basic characteristics of clinical feature: 'RADIATION_THERAPY'

RADIATION_THERAPY Labels N
  NO 125
  YES 42
     
  Significant markers N = 30
  Higher in YES 30
  Higher in NO 0
List of top 10 genes differentially expressed by 'RADIATION_THERAPY'

Table S14.  Get Full Table List of top 10 genes differentially expressed by 'RADIATION_THERAPY'

W(pos if higher in 'YES') wilcoxontestP Q AUC
BRE 3956 9.219e-07 0.00632 0.7535
LOC100302650 3956 9.219e-07 0.00632 0.7535
RBKS 3956 9.219e-07 0.00632 0.7535
AEN 3898 2.683e-06 0.0138 0.7425
CCPG1 3861 5.184e-06 0.0156 0.7354
FOXA2 3841 7.345e-06 0.0156 0.7316
APTX 3833 8.431e-06 0.0156 0.7301
OCLN 3830 8.877e-06 0.0156 0.7295
CORO1B 3826 9.506e-06 0.0156 0.7288
PDIK1L 3821 1.035e-05 0.0156 0.7278
Clinical variable #9: 'KARNOFSKY_PERFORMANCE_SCORE'

30 genes related to 'KARNOFSKY_PERFORMANCE_SCORE'.

Table S15.  Basic characteristics of clinical feature: 'KARNOFSKY_PERFORMANCE_SCORE'

KARNOFSKY_PERFORMANCE_SCORE Mean (SD) 73.82 (16)
  Significant markers N = 30
  pos. correlated 30
  neg. correlated 0
List of top 10 genes differentially expressed by 'KARNOFSKY_PERFORMANCE_SCORE'

Table S16.  Get Full Table List of top 10 genes significantly correlated to 'KARNOFSKY_PERFORMANCE_SCORE' by Spearman correlation test

SpearmanCorr corrP Q
LOC148189 0.671 3.81e-10 7.84e-06
C1D 0.6579 1.085e-09 1.12e-05
GFM1__1 0.6518 1.737e-09 1.19e-05
NR2C1 0.6438 3.167e-09 1.63e-05
FLJ36031 0.6306 1.391e-08 5.23e-05
GORAB 0.6148 2.436e-08 5.23e-05
DEPDC4__1 0.6127 2.811e-08 5.23e-05
SCYL2__1 0.6127 2.811e-08 5.23e-05
COPS2 0.6115 3.036e-08 5.23e-05
GALK2__1 0.6115 3.036e-08 5.23e-05
Clinical variable #10: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

Table S17.  Basic characteristics of clinical feature: 'HISTOLOGICAL_TYPE'

HISTOLOGICAL_TYPE Labels N
  ESOPHAGUS ADENOCARCINOMA NOS 89
  ESOPHAGUS SQUAMOUS CELL CARCINOMA 96
     
  Significant markers N = 30
  Higher in ESOPHAGUS SQUAMOUS CELL CARCINOMA 30
  Higher in ESOPHAGUS ADENOCARCINOMA NOS 0
List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

Table S18.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

W(pos if higher in 'ESOPHAGUS SQUAMOUS CELL CARCINOMA') wilcoxontestP Q AUC
TMED6 c("8525", "1.512e-31") c("8525", "1.512e-31") 1.71e-27 0.9978
GLYCTK c("8522", "1.666e-31") c("8522", "1.666e-31") 1.71e-27 0.9974
RAB11FIP4 c("8488", "4.976e-31") c("8488", "4.976e-31") 3.03e-27 0.9934
DST c("72", "8.305e-31") c("72", "8.305e-31") 3.03e-27 0.9916
WNT4 c("80", "1.072e-30") c("80", "1.072e-30") 3.03e-27 0.9906
AP2A2 c("8460", "1.218e-30") c("8460", "1.218e-30") 3.03e-27 0.9902
KIAA1804 c("8457", "1.34e-30") c("8457", "1.34e-30") 3.03e-27 0.9898
FZD5 c("8455", "1.428e-30") c("8455", "1.428e-30") 3.03e-27 0.9896
GPR44 c("8454", "1.474e-30") c("8454", "1.474e-30") 3.03e-27 0.9895
PLS1 c("8453", "1.522e-30") c("8453", "1.522e-30") 3.03e-27 0.9893
Clinical variable #11: 'NUMBER_PACK_YEARS_SMOKED'

30 genes related to 'NUMBER_PACK_YEARS_SMOKED'.

Table S19.  Basic characteristics of clinical feature: 'NUMBER_PACK_YEARS_SMOKED'

NUMBER_PACK_YEARS_SMOKED Mean (SD) 34.48 (22)
  Significant markers N = 30
  pos. correlated 2
  neg. correlated 28
List of top 10 genes differentially expressed by 'NUMBER_PACK_YEARS_SMOKED'

Table S20.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_PACK_YEARS_SMOKED' by Spearman correlation test

SpearmanCorr corrP Q
KIAA1530 -0.51 8.115e-08 0.00167
TENC1 -0.4841 4.416e-07 0.00454
D2HGDH -0.4618 1.696e-06 0.0116
MLLT6 -0.4527 2.874e-06 0.0148
C15ORF57 -0.4432 5.464e-06 0.0225
MAPK3 -0.4346 7.757e-06 0.0266
C19ORF23 -0.4252 1.274e-05 0.0328
CIRBP -0.4252 1.274e-05 0.0328
MAP2K3 -0.4143 2.229e-05 0.0476
ABCC10 -0.4135 2.311e-05 0.0476
Clinical variable #12: 'RESIDUAL_TUMOR'

No gene related to 'RESIDUAL_TUMOR'.

Table S21.  Basic characteristics of clinical feature: 'RESIDUAL_TUMOR'

RESIDUAL_TUMOR Labels N
  R0 137
  R1 13
  R2 2
  RX 7
     
  Significant markers N = 0
Clinical variable #13: 'NUMBER_OF_LYMPH_NODES'

No gene related to 'NUMBER_OF_LYMPH_NODES'.

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

NUMBER_OF_LYMPH_NODES Mean (SD) 2.53 (3.4)
  Significant markers N = 0
Clinical variable #14: 'RACE'

30 genes related to 'RACE'.

Table S23.  Basic characteristics of clinical feature: 'RACE'

RACE Labels N
  ASIAN 46
  BLACK OR AFRICAN AMERICAN 5
  WHITE 114
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

Table S24.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
GATM 1.343e-13 1.97e-09
YEATS2 1.917e-13 1.97e-09
HABP4 5.796e-13 3.22e-09
RIMS2 6.258e-13 3.22e-09
DCUN1D1 9.205e-13 3.29e-09
CTBP2 1.302e-12 3.29e-09
TMEM108 1.303e-12 3.29e-09
RASSF3 1.604e-12 3.29e-09
LASP1 1.894e-12 3.29e-09
HAND2__1 1.908e-12 3.29e-09
Clinical variable #15: 'ETHNICITY'

No gene related to 'ETHNICITY'.

Table S25.  Basic characteristics of clinical feature: 'ETHNICITY'

ETHNICITY Labels N
  HISPANIC OR LATINO 6
  NOT HISPANIC OR LATINO 88
     
  Significant markers N = 0
Methods & Data
Input

  • Expresson data file = ESCA-TP.meth.by_min_clin_corr.data.txt

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

  • Number of patients = 185

  • Number of genes = 20580

  • Number of clinical features = 15

Selected clinical features

  • Further details on clinical features selected for this analysis, please find a documentation on selected CDEs (Clinical Data Elements). The first column of the file is a formula to convert values and the second column is a clinical parameter name.

  • Survival time data

    • Survival time data is a combined value of days_to_death and days_to_last_followup. For each patient, it creates a combined value 'days_to_death_or_last_fup' using conversion process below.

      • if 'vital_status'==1(dead), 'days_to_last_followup' is always NA. Thus, uses 'days_to_death' value for 'days_to_death_or_fup'

      • if 'vital_status'==0(alive),

        • if 'days_to_death'==NA & 'days_to_last_followup'!=NA, uses 'days_to_last_followup' value for 'days_to_death_or_fup'

        • if 'days_to_death'!=NA, excludes this case in survival analysis and report the case.

      • if 'vital_status'==NA,excludes this case in survival analysis and report the case.

    • cf. In certain diesase types such as SKCM, days_to_death parameter is replaced with time_from_specimen_dx or time_from_specimen_procurement_to_death .

  • This analysis excluded clinical variables that has only NA values.

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

Wilcoxon rank sum test (Mann-Whitney U test)

For two groups (mutant or wild-type) of continuous type of clinical data, wilcoxon rank sum test (Mann and Whitney, 1947) was applied to compare their mean difference using 'wilcox.test(continuous.clinical ~ as.factor(group), exact=FALSE)' function in R. This test is equivalent to the Mann-Whitney test.

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] Mann and Whitney, On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other, Annals of Mathematical Statistics 18 (1), 50-60 (1947)
[4] 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)
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