Correlation between gene methylation status and clinical features
Stomach Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene methylation status and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C15Q4VJW
Overview
Introduction

This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features. The input file "STAD-TP.meth.by_min_clin_corr.data.txt" is generated in the pipeline Methylation_Preprocess in stddata run.

Summary

Testing the association between 17409 genes and 13 clinical features across 395 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 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • FLJ43663 ,  ERCC1 ,  AMIGO2 ,  GHRL ,  UCP3 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • C14ORF72 ,  MINA ,  EARS2 ,  SIGIRR ,  YIPF2 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • DYNC2LI1 ,  H3F3C ,  URB1 ,  CCDC109B ,  CCDC93 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • GMPR ,  RAB26 ,  KREMEN1 ,  FBXO33 ,  SORD ,  ...

  • 30 genes correlated to 'PATHOLOGY_M_STAGE'.

    • FKBP14 ,  DNTTIP1 ,  JPH2 ,  USP1 ,  CCDC90B ,  ...

  • 30 genes correlated to 'GENDER'.

    • KIF4B ,  GPX1 ,  CHTF8 ,  FRG1B ,  ISOC2 ,  ...

  • 30 genes correlated to 'RADIATION_THERAPY'.

    • RNMT ,  ZNF335 ,  TMEM167B ,  KIAA1109 ,  KCNN4 ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • C3ORF26 ,  CDH22 ,  KRT23 ,  C20ORF151 ,  CRLS1 ,  ...

  • 30 genes correlated to 'RESIDUAL_TUMOR'.

    • ERCC2 ,  BRWD1 ,  MAP3K11 ,  CCDC144A ,  C2ORF27A ,  ...

  • 30 genes correlated to 'RACE'.

    • FAM63B ,  ZNF48 ,  ZYG11B ,  CRYZ ,  YIPF1 ,  ...

  • No genes correlated to 'PATHOLOGY_N_STAGE', '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=30   N=NA   N=NA
YEARS_TO_BIRTH Spearman correlation test N=30 older N=0 younger N=30
PATHOLOGIC_STAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=16 lower stage N=14
PATHOLOGY_N_STAGE Spearman correlation test   N=0        
PATHOLOGY_M_STAGE Wilcoxon test N=30 class1 N=30 class0 N=0
GENDER Wilcoxon test N=30 male N=30 female N=0
RADIATION_THERAPY Wilcoxon test N=30 yes N=30 no N=0
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
RESIDUAL_TUMOR Kruskal-Wallis test N=30        
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'

30 genes 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) 0.1-122.3 (median=15.3)
  censored N = 239
  death N = 155
     
  Significant markers N = 30
  associated with shorter survival NA
  associated with longer survival NA
List of top 10 genes differentially expressed by 'DAYS_TO_DEATH_OR_LAST_FUP'

Table S2.  Get Full Table List of top 10 genes significantly associated with 'Time to Death' by Cox regression test. For the survival curves, it compared quantile intervals at c(0, 0.25, 0.50, 0.75, 1) and did not try survival analysis if there is only one interval.

logrank_P Q C_index
FLJ43663 5.58e-06 0.061 0.516
ERCC1 8.78e-06 0.061 0.508
AMIGO2 1.05e-05 0.061 0.431
GHRL 3.68e-05 0.15 0.449
UCP3 4.31e-05 0.15 0.461
IFFO2 5.01e-05 0.15 0.499
FAM167B 8.47e-05 0.16 0.463
ABCA1 0.000105 0.16 0.394
BMP6 0.000115 0.16 0.415
ARHGEF17 0.000118 0.16 0.404
Clinical variable #2: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

Table S3.  Basic characteristics of clinical feature: 'YEARS_TO_BIRTH'

YEARS_TO_BIRTH Mean (SD) 65.21 (11)
  Significant markers N = 30
  pos. correlated 0
  neg. correlated 30
List of top 10 genes differentially expressed by 'YEARS_TO_BIRTH'

Table S4.  Get Full Table List of top 10 genes significantly correlated to 'YEARS_TO_BIRTH' by Spearman correlation test

SpearmanCorr corrP Q
C14ORF72 -0.2888 7.462e-09 0.00013
MINA -0.2642 1.385e-07 0.000885
EARS2 -0.2615 1.859e-07 0.000885
SIGIRR -0.2572 2.997e-07 0.000885
YIPF2 -0.2545 4.038e-07 0.000885
STARD10 -0.2543 4.109e-07 0.000885
C13ORF36 -0.2535 4.481e-07 0.000885
C20ORF186 -0.251 5.868e-07 0.000885
NRARP -0.251 5.891e-07 0.000885
ATG9B -0.2506 6.109e-07 0.000885
Clinical variable #3: 'PATHOLOGIC_STAGE'

30 genes related to 'PATHOLOGIC_STAGE'.

Table S5.  Basic characteristics of clinical feature: 'PATHOLOGIC_STAGE'

PATHOLOGIC_STAGE Labels N
  STAGE I 2
  STAGE IA 15
  STAGE IB 35
  STAGE II 29
  STAGE IIA 41
  STAGE IIB 55
  STAGE III 2
  STAGE IIIA 75
  STAGE IIIB 62
  STAGE IIIC 38
  STAGE IV 33
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

Table S6.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

kruskal_wallis_P Q
DYNC2LI1 6.924e-08 0.00063
H3F3C 7.238e-08 0.00063
URB1 1.432e-07 0.000831
CCDC109B 2.003e-07 0.000864
CCDC93 2.768e-07 0.000864
MRPS36 3.47e-07 0.000864
C10ORF110 3.474e-07 0.000864
KIAA2026 8.377e-07 0.00182
TRNT1 1.046e-06 0.00202
RPL34 1.242e-06 0.00208
Clinical variable #4: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

Table S7.  Basic characteristics of clinical feature: 'PATHOLOGY_T_STAGE'

PATHOLOGY_T_STAGE Mean (SD) 2.97 (0.83)
  N
  T1 21
  T2 78
  T3 186
  T4 110
     
  Significant markers N = 30
  pos. correlated 16
  neg. correlated 14
List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S8.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
GMPR 0.2945 2.415e-09 2.44e-05
RAB26 0.2933 2.801e-09 2.44e-05
KREMEN1 0.2813 1.286e-08 7.46e-05
FBXO33 -0.277 2.179e-08 8.31e-05
SORD 0.2758 2.521e-08 8.31e-05
LRRC40 -0.2747 2.864e-08 8.31e-05
SNORA21 -0.2637 1.043e-07 0.000256
RPL24 -0.2627 1.177e-07 0.000256
SRP14 -0.2606 1.493e-07 0.000281
LOC723972 0.2599 1.613e-07 0.000281
Clinical variable #5: 'PATHOLOGY_N_STAGE'

No gene related to 'PATHOLOGY_N_STAGE'.

Table S9.  Basic characteristics of clinical feature: 'PATHOLOGY_N_STAGE'

PATHOLOGY_N_STAGE Mean (SD) 1.31 (1.1)
  N
  N0 124
  N1 101
  N2 80
  N3 83
     
  Significant markers N = 0
Clinical variable #6: 'PATHOLOGY_M_STAGE'

30 genes related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 353
  class1 23
     
  Significant markers N = 30
  Higher in class1 30
  Higher in class0 0
List of top 10 genes differentially expressed by 'PATHOLOGY_M_STAGE'

Table S11.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY_M_STAGE'

W(pos if higher in 'class1') wilcoxontestP Q AUC
FKBP14 6311 8.311e-06 0.132 0.7773
DNTTIP1 6161 3.182e-05 0.132 0.7588
JPH2 2010 4.97e-05 0.132 0.7524
USP1 6109 4.97e-05 0.132 0.7524
CCDC90B 6100 5.363e-05 0.132 0.7513
TEX12 2025 5.641e-05 0.132 0.7506
HNRNPR 6059 6.558e-05 0.132 0.7484
C15ORF28 6071 6.839e-05 0.132 0.7478
ZMYM6 6048 8.276e-05 0.132 0.7449
ZNF224 6038 8.985e-05 0.132 0.7437
Clinical variable #7: 'GENDER'

30 genes related to 'GENDER'.

Table S12.  Basic characteristics of clinical feature: 'GENDER'

GENDER Labels N
  FEMALE 136
  MALE 259
     
  Significant markers N = 30
  Higher in MALE 30
  Higher in FEMALE 0
List of top 10 genes differentially expressed by 'GENDER'

Table S13.  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 7059 1.272e-22 2.21e-18 0.7996
GPX1 7342 1.648e-21 1.43e-17 0.7916
CHTF8 27072 1.726e-18 1e-14 0.7686
FRG1B 9242 8.302e-15 3.61e-11 0.7376
ISOC2 24097 1.804e-09 6.28e-06 0.6841
GPN1 11169 2.293e-09 6.65e-06 0.6829
RIMBP3 23629 2.399e-08 5.97e-05 0.6708
NCRNA00116 12004 1.981e-07 0.000431 0.6592
FAM117B 12278 7.539e-07 0.00146 0.6514
VPS54 12327 9.512e-07 0.00166 0.65
Clinical variable #8: 'RADIATION_THERAPY'

30 genes related to 'RADIATION_THERAPY'.

Table S14.  Basic characteristics of clinical feature: 'RADIATION_THERAPY'

RADIATION_THERAPY Labels N
  NO 302
  YES 75
     
  Significant markers N = 30
  Higher in YES 30
  Higher in NO 0
List of top 10 genes differentially expressed by 'RADIATION_THERAPY'

Table S15.  Get Full Table List of top 10 genes differentially expressed by 'RADIATION_THERAPY'

W(pos if higher in 'YES') wilcoxontestP Q AUC
RNMT 6412 6.033e-09 0.000105 0.7169
ZNF335 7095 5.521e-07 0.0033 0.6868
TMEM167B 7100 5.693e-07 0.0033 0.6865
KIAA1109 7221 1.185e-06 0.00516 0.6812
KCNN4 7271 1.595e-06 0.00556 0.679
NCF1B 7337 2.35e-06 0.00682 0.6761
SLC39A9 7418 3.749e-06 0.00848 0.6725
FAM194A 7399 3.899e-06 0.00848 0.6722
H1FX 7452 4.548e-06 0.0088 0.671
CORO7 7504 6.096e-06 0.0106 0.6687
Clinical variable #9: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE 13
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE 67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) 135
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) 73
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE 8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE 78
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

Table S17.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

kruskal_wallis_P Q
C3ORF26 6.404e-13 1.11e-08
CDH22 1.411e-11 8.73e-08
KRT23 1.505e-11 8.73e-08
C20ORF151 2.665e-11 1.03e-07
CRLS1 3.525e-11 1.03e-07
LCT 3.891e-11 1.03e-07
C20ORF54 4.133e-11 1.03e-07
SLC23A1 5.066e-11 1.1e-07
RAB19 8.049e-11 1.48e-07
C1ORF170 9.251e-11 1.48e-07
Clinical variable #10: 'RESIDUAL_TUMOR'

30 genes related to 'RESIDUAL_TUMOR'.

Table S18.  Basic characteristics of clinical feature: 'RESIDUAL_TUMOR'

RESIDUAL_TUMOR Labels N
  R0 335
  R1 17
  R2 12
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RESIDUAL_TUMOR'

Table S19.  Get Full Table List of top 10 genes differentially expressed by 'RESIDUAL_TUMOR'

kruskal_wallis_P Q
ERCC2 1.754e-05 0.211
BRWD1 2.429e-05 0.211
MAP3K11 4.301e-05 0.226
CCDC144A 8.665e-05 0.226
C2ORF27A 9.733e-05 0.226
XPNPEP3 0.0001013 0.226
MATN4 0.0001654 0.226
SCP2 0.000189 0.226
MGC2889 0.0001932 0.226
SNRNP35 0.000289 0.226
Clinical variable #11: 'NUMBER_OF_LYMPH_NODES'

No gene related to 'NUMBER_OF_LYMPH_NODES'.

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

NUMBER_OF_LYMPH_NODES Mean (SD) 5.6 (8.4)
  Significant markers N = 0
Clinical variable #12: 'RACE'

30 genes related to 'RACE'.

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

RACE Labels N
  ASIAN 89
  BLACK OR AFRICAN AMERICAN 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 1
  WHITE 253
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

Table S22.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
FAM63B 1.491e-20 2.6e-16
ZNF48 3.757e-18 3.27e-14
ZYG11B 8.264e-18 4.8e-14
CRYZ 1.486e-16 6.47e-13
YIPF1 3.207e-16 1.12e-12
WDR6 6.461e-15 1.87e-11
NBPF1 8.674e-15 2.12e-11
LOC100271836 9.719e-15 2.12e-11
XAB2 1.621e-14 3.13e-11
NCF1B 1.922e-14 3.35e-11
Clinical variable #13: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 5
  NOT HISPANIC OR LATINO 293
     
  Significant markers N = 0
Methods & Data
Input
  • Expresson data file = STAD-TP.meth.by_min_clin_corr.data.txt

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

  • Number of patients = 395

  • Number of genes = 17409

  • Number of clinical features = 13

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, logrank test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values comparing quantile intervals using the 'coxph' function in R. Kaplan-Meier survival curves were plotted using quantile intervals at c(0, 0.25, 0.50, 0.75, 1). If there is only one interval group, it will not try survival analysis.

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)