Correlation between gene methylation status and clinical features
Colon Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C15T3JGX
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/C15T3JGX
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 19882 genes and 12 clinical features across 288 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 8 clinical features related to at least one genes.

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • GDNF ,  OTUD7A ,  C1QL1 ,  SLC26A8 ,  KLF14 ,  ...

  • 22 genes correlated to 'NEOPLASM_DISEASESTAGE'.

    • C8ORF80 ,  UBE2L6 ,  SP140L ,  IL12RB1 ,  APOL1 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • CASP1__1 ,  UBE2L6 ,  APOL1 ,  IL12RB1 ,  MED18 ,  ...

  • 30 genes correlated to 'PATHOLOGY_M_STAGE'.

    • KIF13B ,  ARAP2 ,  PBK ,  PHC2 ,  PSORS1C1__2 ,  ...

  • 30 genes correlated to 'GENDER'.

    • GPX1 ,  KIF4B ,  POLDIP3 ,  RNU12 ,  MIR220B ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • POFUT1 ,  MYST4 ,  PDE4B ,  RALGPS1__1 ,  POLR1D ,  ...

  • 30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

    • CASP1__1 ,  UBE2L6 ,  IL12RB1 ,  APOL1 ,  CSGALNACT1 ,  ...

  • 30 genes correlated to 'RACE'.

    • SMARCC2 ,  C14ORF167 ,  DHRS4 ,  DHRS7 ,  GSTCD__1 ,  ...

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

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
NEOPLASM_DISEASESTAGE Kruskal-Wallis test N=22        
PATHOLOGY_T_STAGE Spearman correlation test   N=0        
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 Wilcoxon test N=30 colon mucinous adenocarcinoma N=30 colon adenocarcinoma N=0
RADIATIONS_RADIATION_REGIMENINDICATION Wilcoxon test   N=0        
COMPLETENESS_OF_RESECTION Kruskal-Wallis test   N=0        
NUMBER_OF_LYMPH_NODES Spearman correlation test N=30 higher number_of_lymph_nodes N=29 lower number_of_lymph_nodes N=1
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=20)
  censored N = 225
  death N = 62
     
  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) 64.91 (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 0.3044 1.51e-07 0.00275
OTUD7A 0.2982 2.768e-07 0.00275
C1QL1 0.2834 1.102e-06 0.00679
SLC26A8 0.2807 1.409e-06 0.00679
KLF14 0.2786 1.708e-06 0.00679
GPR1 0.2752 2.293e-06 0.00733
TAC1 0.2739 2.58e-06 0.00733
LRRC55 0.2699 3.65e-06 0.00892
VENTX 0.2687 4.036e-06 0.00892
EBF4 0.2607 7.902e-06 0.0154
Clinical variable #3: 'NEOPLASM_DISEASESTAGE'

22 genes related to 'NEOPLASM_DISEASESTAGE'.

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

NEOPLASM_DISEASESTAGE Labels N
  STAGE I 43
  STAGE IA 1
  STAGE II 14
  STAGE IIA 92
  STAGE IIB 5
  STAGE IIC 1
  STAGE III 7
  STAGE IIIA 9
  STAGE IIIB 44
  STAGE IIIC 24
  STAGE IV 21
  STAGE IVA 17
  STAGE IVB 2
     
  Significant markers N = 22
List of top 10 genes differentially expressed by 'NEOPLASM_DISEASESTAGE'

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

kruskal_wallis_P Q
C8ORF80 4.908e-07 0.00976
UBE2L6 1.024e-06 0.0102
SP140L 3.94e-05 0.203
IL12RB1 4.177e-05 0.203
APOL1 5.109e-05 0.203
TERF2 7.184e-05 0.227
ASPHD2 0.0001012 0.227
FBXL19 0.0001026 0.227
NCRNA00095 0.0001026 0.227
MLLT1 0.0001466 0.267
Clinical variable #4: 'PATHOLOGY_T_STAGE'

No gene related to 'PATHOLOGY_T_STAGE'.

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

PATHOLOGY_T_STAGE Mean (SD) 2.93 (0.62)
  N
  T1 7
  T2 44
  T3 198
  T4 38
     
  Significant markers N = 0
Clinical variable #5: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

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

PATHOLOGY_N_STAGE Mean (SD) 0.59 (0.76)
  N
  N0 167
  N1 72
  N2 48
     
  Significant markers N = 30
  pos. correlated 24
  neg. correlated 6
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

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

SpearmanCorr corrP Q
CASP1__1 0.3588 3.809e-10 7.57e-06
UBE2L6 0.3374 4.507e-09 4.48e-05
APOL1 0.3131 6.008e-08 0.000398
IL12RB1 0.2932 4.27e-07 0.00212
MED18 0.2866 7.923e-07 0.00315
ASPHD2 0.2836 1.038e-06 0.00344
CASP5 0.2778 1.752e-06 0.00487
PKN2 0.2762 2.013e-06 0.00487
PFKFB2 0.2751 2.223e-06 0.00487
SP140L 0.274 2.449e-06 0.00487
Clinical variable #6: 'PATHOLOGY_M_STAGE'

30 genes related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 192
  class1 39
     
  Significant markers N = 30
  Higher in class1 30
  Higher in class0 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 'class1') wilcoxontestP Q AUC
KIF13B 5542 1.6e-06 0.017 0.744
ARAP2 5565 1.712e-06 0.017 0.7432
PBK 5502 3.854e-06 0.0255 0.7348
PHC2 2067 1.052e-05 0.0345 0.724
PSORS1C1__2 2090 1.388e-05 0.0345 0.7209
PSORS1C2__1 2090 1.388e-05 0.0345 0.7209
PURG 5395 1.439e-05 0.0345 0.7205
WRN 5395 1.439e-05 0.0345 0.7205
IL17D 2100 1.564e-05 0.0345 0.7196
SMAD4 5232 2.737e-05 0.0508 0.7136
Clinical variable #7: 'GENDER'

30 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 133
  MALE 155
     
  Significant markers N = 30
  Higher in MALE 30
  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
GPX1 3392 9.809e-23 1.95e-18 0.8355
KIF4B 4075 9.187e-19 9.13e-15 0.8023
POLDIP3 4332 2.255e-17 1.12e-13 0.7899
RNU12 4332 2.255e-17 1.12e-13 0.7899
MIR220B 15564 8.69e-14 2.88e-10 0.755
TUBB4 15564 8.69e-14 2.88e-10 0.755
PSRC1 5486 7.806e-12 2.22e-08 0.7339
PAFAH1B2 5704 6.461e-11 1.61e-07 0.7233
ZNF839 6724 3.675e-07 0.000771 0.6738
FASTKD2 6744 4.266e-07 0.000771 0.6729
Clinical variable #8: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  COLON ADENOCARCINOMA 250
  COLON MUCINOUS ADENOCARCINOMA 38
     
  Significant markers N = 30
  Higher in COLON MUCINOUS ADENOCARCINOMA 30
  Higher in COLON ADENOCARCINOMA 0
List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

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

W(pos if higher in 'COLON MUCINOUS ADENOCARCINOMA') wilcoxontestP Q AUC
POFUT1 7278 1.263e-07 0.00251 0.7661
MYST4 2340 4.719e-07 0.00277 0.7537
PDE4B 2345 4.983e-07 0.00277 0.7532
RALGPS1__1 7126 6.823e-07 0.00277 0.7501
POLR1D 7124 6.972e-07 0.00277 0.7499
BCL2L1 7061 1.362e-06 0.00451 0.7433
SPDYC 2457 1.645e-06 0.00466 0.7414
B3GNT6 2480 2.088e-06 0.00466 0.7389
REV1 7019 2.11e-06 0.00466 0.7388
C19ORF12 7007 2.387e-06 0.00475 0.7376
Clinical variable #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

No gene related to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

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

RADIATIONS_RADIATION_REGIMENINDICATION Labels N
  NO 3
  YES 285
     
  Significant markers N = 0
Clinical variable #10: 'COMPLETENESS_OF_RESECTION'

No gene related to 'COMPLETENESS_OF_RESECTION'.

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

COMPLETENESS_OF_RESECTION Labels N
  R0 187
  R1 2
  R2 4
  RX 24
     
  Significant markers N = 0
Clinical variable #11: 'NUMBER_OF_LYMPH_NODES'

30 genes related to 'NUMBER_OF_LYMPH_NODES'.

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

NUMBER_OF_LYMPH_NODES Mean (SD) 2 (4.5)
  Significant markers N = 30
  pos. correlated 29
  neg. correlated 1
List of top 10 genes differentially expressed by 'NUMBER_OF_LYMPH_NODES'

Table S18.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_OF_LYMPH_NODES' by Spearman correlation test

SpearmanCorr corrP Q
CASP1__1 0.3763 2.626e-10 5.22e-06
UBE2L6 0.3499 5.104e-09 5.07e-05
IL12RB1 0.3126 2.158e-07 0.00143
APOL1 0.3079 3.332e-07 0.00166
CSGALNACT1 0.2902 1.615e-06 0.00642
C8ORF80 0.2782 4.456e-06 0.0132
PKN2 0.2776 4.665e-06 0.0132
RARRES3 0.2748 5.884e-06 0.0134
SRBD1 0.2734 6.591e-06 0.0134
CARD16 0.2717 7.51e-06 0.0134
Clinical variable #12: 'RACE'

30 genes related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 1
  ASIAN 11
  BLACK OR AFRICAN AMERICAN 53
  WHITE 205
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

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

kruskal_wallis_P Q
SMARCC2 1.888e-18 3.75e-14
C14ORF167 4.996e-13 3.31e-09
DHRS4 4.996e-13 3.31e-09
DHRS7 5.248e-12 2.61e-08
GSTCD__1 1.005e-10 2.86e-07
INTS12__1 1.005e-10 2.86e-07
LOC100133161 1.005e-10 2.86e-07
PGBD5 5.497e-10 1.37e-06
XPNPEP1 7.653e-10 1.69e-06
PLA2G4C 8.936e-10 1.78e-06
Methods & Data
Input

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

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

  • Number of patients = 288

  • Number of genes = 19882

  • Number of clinical features = 12

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)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle