Correlation between gene methylation status and clinical features
Colorectal Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C13R0RWB
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/C13R0RWB
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 19878 genes and 13 clinical features across 386 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 11 clinical features related to at least one genes.

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • GDNF ,  KLF14 ,  OTUD7A ,  IDO2 ,  EBF4 ,  ...

  • 30 genes correlated to 'PRIMARY_SITE_OF_DISEASE'.

    • PAPLN ,  SMPD1 ,  FAM13C ,  FLJ13197__1 ,  KLF3__1 ,  ...

  • 30 genes correlated to 'NEOPLASM_DISEASESTAGE'.

    • UBE2L6 ,  SP140L ,  C8ORF80 ,  APOL1 ,  DPCR1 ,  ...

  • 3 genes correlated to 'PATHOLOGY_T_STAGE'.

    • SYN2 ,  TIMP4 ,  PHYHIP

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • UBE2L6 ,  CASP1__2 ,  SP140L ,  CASP5 ,  APOL1 ,  ...

  • 30 genes correlated to 'PATHOLOGY_M_STAGE'.

    • UBE2L6 ,  SP140L ,  IRF1 ,  TFAP2C ,  ARAP2 ,  ...

  • 30 genes correlated to 'GENDER'.

    • GPX1 ,  KIF4B ,  MIR220B ,  TUBB4 ,  PAFAH1B2 ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • SMPD1 ,  PAPLN ,  FAM13C ,  C20ORF43__1 ,  ZNF335 ,  ...

  • 11 genes correlated to 'COMPLETENESS_OF_RESECTION'.

    • RIPK2 ,  BCAS4 ,  BLOC1S3__1 ,  TRAPPC6A ,  LOC642502 ,  ...

  • 30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

    • CASP1__2 ,  UBE2L6 ,  IL12RB1 ,  RARRES3 ,  ACTA2__1 ,  ...

  • 30 genes correlated to 'RACE'.

    • GSTCD__1 ,  INTS12__1 ,  DHRS7 ,  F12 ,  IL20 ,  ...

  • No genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

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=30 younger N=0
PRIMARY_SITE_OF_DISEASE Wilcoxon test N=30 rectum N=30 colon N=0
NEOPLASM_DISEASESTAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=3 higher stage N=2 lower stage N=1
PATHOLOGY_N_STAGE Spearman correlation test N=30 higher stage N=24 lower stage N=6
PATHOLOGY_M_STAGE Wilcoxon test N=30 class1 N=30 class0 N=0
GENDER Wilcoxon test N=30 male N=30 female N=0
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
RADIATIONS_RADIATION_REGIMENINDICATION Wilcoxon test   N=0        
COMPLETENESS_OF_RESECTION Kruskal-Wallis test N=11        
NUMBER_OF_LYMPH_NODES Spearman correlation test N=30 higher number_of_lymph_nodes N=26 lower number_of_lymph_nodes N=4
RACE Kruskal-Wallis test N=30        
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) 0.1-140.4 (median=17.8)
  censored N = 311
  death N = 74
     
  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) 64.4 (13)
  Significant markers N = 30
  pos. correlated 30
  neg. correlated 0
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
GDNF 0.2919 5.55e-09 0.00011
KLF14 0.2814 2.027e-08 0.000202
OTUD7A 0.2638 1.565e-07 0.00104
IDO2 0.2596 2.49e-07 0.00124
EBF4 0.2528 5.181e-07 0.00185
ELOVL2 0.2521 5.59e-07 0.00185
FOXC2 0.2499 7.022e-07 0.00199
VENTX 0.2467 9.827e-07 0.00244
PENK 0.2441 1.295e-06 0.00286
ZNF334 0.243 1.448e-06 0.00288
Clinical variable #3: 'PRIMARY_SITE_OF_DISEASE'

30 genes related to 'PRIMARY_SITE_OF_DISEASE'.

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

PRIMARY_SITE_OF_DISEASE Labels N
  COLON 288
  RECTUM 96
     
  Significant markers N = 30
  Higher in RECTUM 30
  Higher in COLON 0
List of top 10 genes differentially expressed by 'PRIMARY_SITE_OF_DISEASE'

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

W(pos if higher in 'RECTUM') wilcoxontestP Q AUC
PAPLN 3530 8.351e-28 8.8e-24 0.8723
SMPD1 3535 8.854e-28 8.8e-24 0.8721
FAM13C 3642 3.075e-27 2.04e-23 0.8683
FLJ13197__1 4221 2.075e-24 8.25e-21 0.8473
KLF3__1 4221 2.075e-24 8.25e-21 0.8473
MED27 4258 3.106e-24 1.03e-20 0.846
PRKAR2A 4286 4.211e-24 1.2e-20 0.845
METTL3 23076 1.004e-23 2.25e-20 0.8434
TEF 4372 1.067e-23 2.25e-20 0.8419
FOXC1 4358 1.13e-23 2.25e-20 0.8418
Clinical variable #4: 'NEOPLASM_DISEASESTAGE'

30 genes related to 'NEOPLASM_DISEASESTAGE'.

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

NEOPLASM_DISEASESTAGE Labels N
  STAGE I 54
  STAGE IA 1
  STAGE II 20
  STAGE IIA 112
  STAGE IIB 7
  STAGE IIC 3
  STAGE III 11
  STAGE IIIA 18
  STAGE IIIB 57
  STAGE IIIC 35
  STAGE IV 27
  STAGE IVA 26
  STAGE IVB 2
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'NEOPLASM_DISEASESTAGE'

Table S7.  Get Full Table List of top 10 genes differentially expressed by 'NEOPLASM_DISEASESTAGE'

kruskal_wallis_P Q
UBE2L6 2.947e-09 5.86e-05
SP140L 4.481e-07 0.00445
C8ORF80 6.752e-07 0.00447
APOL1 3.383e-06 0.0168
DPCR1 7.538e-06 0.03
RARRES3 1.305e-05 0.0387
CASP1__2 1.364e-05 0.0387
SCEL 3.333e-05 0.0828
IL12RB1 4.741e-05 0.105
CASP5 5.415e-05 0.108
Clinical variable #5: 'PATHOLOGY_T_STAGE'

3 genes related to 'PATHOLOGY_T_STAGE'.

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

PATHOLOGY_T_STAGE Mean (SD) 2.92 (0.62)
  N
  T1 11
  T2 57
  T3 267
  T4 49
     
  Significant markers N = 3
  pos. correlated 2
  neg. correlated 1
List of 3 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S9.  Get Full Table List of 3 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
SYN2 0.2475 9.096e-07 0.00904
TIMP4 0.2475 9.096e-07 0.00904
PHYHIP -0.2182 1.609e-05 0.107
Clinical variable #6: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

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

PATHOLOGY_N_STAGE Mean (SD) 0.63 (0.77)
  N
  N0 210
  N1 102
  N2 70
     
  Significant markers N = 30
  pos. correlated 24
  neg. correlated 6
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

Table S11.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_N_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
UBE2L6 0.3489 2.231e-12 4.43e-08
CASP1__2 0.3392 9.75e-12 9.69e-08
SP140L 0.2972 3.135e-09 2.08e-05
CASP5 0.2908 7.004e-09 3.48e-05
APOL1 0.2818 2.092e-08 7.14e-05
IL12RB1 0.2816 2.155e-08 7.14e-05
MARCH8 0.2783 3.193e-08 8.89e-05
RARRES3 0.2773 3.577e-08 8.89e-05
ASPHD2 0.2761 4.117e-08 9.09e-05
C8ORF80 0.2718 6.756e-08 0.000134
Clinical variable #7: 'PATHOLOGY_M_STAGE'

30 genes related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 262
  class1 51
     
  Significant markers N = 30
  Higher in class1 30
  Higher in class0 0
List of top 10 genes differentially expressed by 'PATHOLOGY_M_STAGE'

Table S13.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY_M_STAGE'

W(pos if higher in 'class1') wilcoxontestP Q AUC
UBE2L6 9666 4.48e-07 0.00891 0.7234
SP140L 9253 1.368e-05 0.102 0.6925
IRF1 9185 2.297e-05 0.102 0.6874
TFAP2C 4188 2.495e-05 0.102 0.6866
ARAP2 9097 4.407e-05 0.102 0.6808
CASP1__2 9068 5.437e-05 0.102 0.6786
SMAD4 8739 5.616e-05 0.102 0.6801
PLAT 4305 5.884e-05 0.102 0.6778
MXI1 8991 7.408e-05 0.102 0.6755
C20ORF202 4349 8.047e-05 0.102 0.6745
Clinical variable #8: 'GENDER'

30 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 177
  MALE 209
     
  Significant markers N = 30
  Higher in MALE 30
  Higher in FEMALE 0
List of top 10 genes differentially expressed by 'GENDER'

Table S15.  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
GPX1 6598 1.244e-27 2.47e-23 0.8216
KIF4B 7280 9.756e-25 9.7e-21 0.8032
MIR220B 28015 2.932e-18 1.46e-14 0.7573
TUBB4 28015 2.932e-18 1.46e-14 0.7573
PAFAH1B2 11056 9.653e-12 3.84e-08 0.7011
UGDH 12584 6.21e-08 0.000206 0.6598
DDX43 12823 2.06e-07 0.000585 0.6534
ZNF839 12851 2.364e-07 0.000587 0.6526
WBP11P1 23967 5.5e-07 0.00121 0.6479
FASTKD2 13067 6.68e-07 0.00121 0.6468
Clinical variable #9: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  COLON ADENOCARCINOMA 250
  COLON MUCINOUS ADENOCARCINOMA 38
  RECTAL ADENOCARCINOMA 90
  RECTAL MUCINOUS ADENOCARCINOMA 6
     
  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
SMPD1 1.532e-26 2.52e-22
PAPLN 2.531e-26 2.52e-22
FAM13C 1.289e-25 8.54e-22
C20ORF43__1 2.555e-25 1.27e-21
ZNF335 3.491e-23 1.39e-19
FOXC1 5.84e-23 1.56e-19
FLJ13197__1 6.259e-23 1.56e-19
KLF3__1 6.259e-23 1.56e-19
MED27 9.516e-23 2.03e-19
CYP19A1 1.022e-22 2.03e-19
Clinical variable #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

No gene related to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

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

RADIATIONS_RADIATION_REGIMENINDICATION Labels N
  NO 8
  YES 378
     
  Significant markers N = 0
Clinical variable #11: 'COMPLETENESS_OF_RESECTION'

11 genes related to 'COMPLETENESS_OF_RESECTION'.

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

COMPLETENESS_OF_RESECTION Labels N
  R0 253
  R1 4
  R2 6
  RX 29
     
  Significant markers N = 11
List of top 10 genes differentially expressed by 'COMPLETENESS_OF_RESECTION'

Table S20.  Get Full Table List of top 10 genes differentially expressed by 'COMPLETENESS_OF_RESECTION'

kruskal_wallis_P Q
RIPK2 9.232e-06 0.0835
BCAS4 1.253e-05 0.0835
BLOC1S3__1 1.68e-05 0.0835
TRAPPC6A 1.68e-05 0.0835
LOC642502 2.969e-05 0.0984
SDHC 2.969e-05 0.0984
RPSAP58 5.996e-05 0.17
FAM55D 7.629e-05 0.189
C7ORF50__2 0.0001011 0.189
LRRIQ1 0.0001047 0.189
Clinical variable #12: 'NUMBER_OF_LYMPH_NODES'

30 genes related to 'NUMBER_OF_LYMPH_NODES'.

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

NUMBER_OF_LYMPH_NODES Mean (SD) 2.28 (4.8)
  Significant markers N = 30
  pos. correlated 26
  neg. correlated 4
List of top 10 genes differentially expressed by 'NUMBER_OF_LYMPH_NODES'

Table S22.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_OF_LYMPH_NODES' by Spearman correlation test

SpearmanCorr corrP Q
CASP1__2 0.3467 2.388e-11 3.98e-07
UBE2L6 0.343 4.006e-11 3.98e-07
IL12RB1 0.295 1.775e-08 0.000118
RARRES3 0.2872 4.302e-08 0.000214
ACTA2__1 0.2756 1.551e-07 0.000496
FAS 0.2756 1.551e-07 0.000496
CASP5 0.274 1.832e-07 0.000496
APOL1 0.2732 1.998e-07 0.000496
MARCH8 0.2691 3.096e-07 0.000657
SP140L 0.2684 3.305e-07 0.000657
Clinical variable #13: 'RACE'

30 genes related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 1
  ASIAN 12
  BLACK OR AFRICAN AMERICAN 58
  WHITE 282
     
  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
GSTCD__1 3.296e-13 3.28e-09
INTS12__1 3.296e-13 3.28e-09
DHRS7 5.853e-13 3.88e-09
F12 2.457e-12 1.22e-08
IL20 3.244e-12 1.29e-08
UBTF 1.793e-10 5.94e-07
TRIM73 2.896e-10 7.16e-07
TRIM74 2.896e-10 7.16e-07
UNG 3.241e-10 7.16e-07
ARL6 6.314e-10 1.26e-06
Methods & Data
Input

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

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

  • Number of patients = 386

  • Number of genes = 19878

  • Number of clinical features = 13

Selected clinical features

  • For clinical features selected for this analysis and their value conozzle.versions, please find a documentation on selected CDEs .

  • 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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