Correlation between gene methylation status and clinical features
Colon/Rectal Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between gene methylation status and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C11N7Z4Z
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 19957 genes and 11 clinical features across 350 samples, statistically thresholded by Q value < 0.05, 11 clinical features related to at least one genes.

  • 1 gene correlated to 'Time to Death'.

    • CTNNB1

  • 10 genes correlated to 'AGE'.

    • GDNF ,  FBXL7 ,  EBF4 ,  ZNF334 ,  FRMD3 ,  ...

  • 1764 genes correlated to 'PRIMARY.SITE.OF.DISEASE'.

    • CCDC85A ,  DCTN5__1 ,  PALB2__1 ,  TEF ,  CATSPER2 ,  ...

  • 10 genes correlated to 'GENDER'.

    • KIF4B ,  GPX1 ,  POLDIP3 ,  RNU12 ,  UBAP2 ,  ...

  • 703 genes correlated to 'HISTOLOGICAL.TYPE'.

    • ZNF646 ,  ZNF668 ,  ZNRF1 ,  METTL3 ,  HIST1H2AL ,  ...

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

    • INHA__1 ,  OBSL1__1 ,  ZNF599 ,  ZNF665 ,  LRGUK ,  ...

  • 284 genes correlated to 'DISTANT.METASTASIS'.

    • JOSD2 ,  FAM86B2 ,  KCNK4 ,  DMKN ,  FZD3 ,  ...

  • 14 genes correlated to 'LYMPH.NODE.METASTASIS'.

    • LLPH ,  ATP5G3 ,  ZNF354A ,  APC ,  LRRC37B2 ,  ...

  • 75 genes correlated to 'COMPLETENESS.OF.RESECTION'.

    • UBE2D4 ,  URGCP__1 ,  TMEM115 ,  GGCT ,  EIF5A ,  ...

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

    • UBE2L6 ,  CASP1__1 ,  IL12RB1 ,  SP140L ,  MAST3 ,  ...

  • 465 genes correlated to 'NEOPLASM.DISEASESTAGE'.

    • JOSD2 ,  FAM86B2 ,  KCNK4 ,  DMKN ,  FZD3 ,  ...

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 Q value < 0.05.

Clinical feature Statistical test Significant genes Associated with                 Associated with
Time to Death Cox regression test N=1 shorter survival N=0 longer survival N=1
AGE Spearman correlation test N=10 older N=10 younger N=0
PRIMARY SITE OF DISEASE t test N=1764 rectum N=217 colon N=1547
GENDER t test N=10 male N=1 female N=9
HISTOLOGICAL TYPE ANOVA test N=703        
RADIATIONS RADIATION REGIMENINDICATION t test N=270 yes N=261 no N=9
DISTANT METASTASIS ANOVA test N=284        
LYMPH NODE METASTASIS ANOVA test N=14        
COMPLETENESS OF RESECTION ANOVA test N=75        
NUMBER OF LYMPH NODES Spearman correlation test N=9 higher number.of.lymph.nodes N=9 lower number.of.lymph.nodes N=0
NEOPLASM DISEASESTAGE ANOVA test N=465        
Clinical variable #1: 'Time to Death'

One gene related to 'Time to Death'.

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

Time to Death Duration (Months) 0.1-135.5 (median=7)
  censored N = 280
  death N = 44
     
  Significant markers N = 1
  associated with shorter survival 0
  associated with longer survival 1
List of one gene significantly associated with 'Time to Death' by Cox regression test

Table S2.  Get Full Table List of one gene significantly associated with 'Time to Death' by Cox regression test

HazardRatio Wald_P Q C_index
CTNNB1 0.01 2.287e-06 0.046 0.399

Figure S1.  Get High-res Image As an example, this figure shows the association of CTNNB1 to 'Time to Death'. four curves present the cumulative survival rates of 4 quartile subsets of patients. P value = 2.29e-06 with univariate Cox regression analysis using continuous log-2 expression values.

Clinical variable #2: 'AGE'

10 genes related to 'AGE'.

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

AGE Mean (SD) 64.75 (13)
  Significant markers N = 10
  pos. correlated 10
  neg. correlated 0
List of 10 genes significantly correlated to 'AGE' by Spearman correlation test

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

SpearmanCorr corrP Q
GDNF 0.2986 1.417e-08 0.000283
FBXL7 0.2709 2.993e-07 0.00597
EBF4 0.266 4.953e-07 0.00988
ZNF334 0.2639 6.128e-07 0.0122
FRMD3 0.2636 6.32e-07 0.0126
ZNF75A 0.2594 9.634e-07 0.0192
APCDD1L 0.259 1.008e-06 0.0201
VIM 0.2587 1.07e-06 0.0213
KIAA1755 0.2577 1.139e-06 0.0227
SYNE1 0.2523 1.935e-06 0.0386

Figure S2.  Get High-res Image As an example, this figure shows the association of GDNF to 'AGE'. P value = 1.42e-08 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'PRIMARY.SITE.OF.DISEASE'

1764 genes related to 'PRIMARY.SITE.OF.DISEASE'.

Table S5.  Basic characteristics of clinical feature: 'PRIMARY.SITE.OF.DISEASE'

PRIMARY.SITE.OF.DISEASE Labels N
  COLON 253
  RECTUM 93
     
  Significant markers N = 1764
  Higher in RECTUM 217
  Higher in COLON 1547
List of top 10 genes differentially expressed by 'PRIMARY.SITE.OF.DISEASE'

Table S6.  Get Full Table List of top 10 genes differentially expressed by 'PRIMARY.SITE.OF.DISEASE'

T(pos if higher in 'RECTUM') ttestP Q AUC
CCDC85A -10.26 5.602e-21 1.12e-16 0.8297
DCTN5__1 -11 7.077e-21 1.41e-16 0.8303
PALB2__1 -11 7.077e-21 1.41e-16 0.8303
TEF -10.16 3.08e-20 6.15e-16 0.8419
CATSPER2 11.06 3.151e-20 6.29e-16 0.8473
ELAVL2 -9.65 1.368e-19 2.73e-15 0.7481
THOP1 9.54 3.087e-19 6.16e-15 0.8547
GHR -9.46 5.078e-19 1.01e-14 0.7656
YWHAQ -9.71 8.62e-19 1.72e-14 0.8226
ACVR2A -9.47 9.391e-19 1.87e-14 0.8147

Figure S3.  Get High-res Image As an example, this figure shows the association of CCDC85A to 'PRIMARY.SITE.OF.DISEASE'. P value = 5.6e-21 with T-test analysis.

Clinical variable #4: 'GENDER'

10 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 155
  MALE 193
     
  Significant markers N = 10
  Higher in MALE 1
  Higher in FEMALE 9
List of 10 genes differentially expressed by 'GENDER'

Table S8.  Get Full Table List of 10 genes differentially expressed by 'GENDER'

T(pos if higher in 'MALE') ttestP Q AUC
KIF4B -11.48 9.581e-26 1.91e-21 0.8108
GPX1 -11.28 2.9e-25 5.79e-21 0.8148
POLDIP3 -10.93 2.096e-23 4.18e-19 0.806
RNU12 -10.93 2.096e-23 4.18e-19 0.806
UBAP2 -7.53 4.694e-13 9.37e-09 0.716
PAFAH1B2 -6.86 3.342e-11 6.67e-07 0.7003
RIMBP3 6.46 3.776e-10 7.53e-06 0.6835
YARS2 -5.18 3.92e-07 0.00782 0.6604
ZNF839 -5 9.021e-07 0.018 0.6532
PRDM4 -4.89 1.628e-06 0.0325 0.7116

Figure S4.  Get High-res Image As an example, this figure shows the association of KIF4B to 'GENDER'. P value = 9.58e-26 with T-test analysis.

Clinical variable #5: 'HISTOLOGICAL.TYPE'

703 genes related to 'HISTOLOGICAL.TYPE'.

Table S9.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  COLON ADENOCARCINOMA 223
  COLON MUCINOUS ADENOCARCINOMA 30
  RECTAL ADENOCARCINOMA 87
  RECTAL MUCINOUS ADENOCARCINOMA 6
     
  Significant markers N = 703
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S10.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
ZNF646 2.805e-42 5.6e-38
ZNF668 2.805e-42 5.6e-38
ZNRF1 2.288e-37 4.57e-33
METTL3 4.547e-37 9.07e-33
HIST1H2AL 1.913e-32 3.82e-28
CATSPER2 5.184e-31 1.03e-26
EEF1DP3 5.353e-28 1.07e-23
C20ORF43__1 2.245e-27 4.48e-23
KIAA1279 5.445e-27 1.09e-22
DCTN5__1 1.497e-26 2.99e-22

Figure S5.  Get High-res Image As an example, this figure shows the association of ZNF646 to 'HISTOLOGICAL.TYPE'. P value = 2.8e-42 with ANOVA analysis.

Clinical variable #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

Table S11.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 8
  YES 342
     
  Significant markers N = 270
  Higher in YES 261
  Higher in NO 9
List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S12.  Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

T(pos if higher in 'YES') ttestP Q AUC
INHA__1 16.14 1.16e-39 2.32e-35 0.7847
OBSL1__1 16.14 1.16e-39 2.32e-35 0.7847
ZNF599 14.8 9.42e-38 1.88e-33 0.7825
ZNF665 13.56 1.186e-33 2.37e-29 0.7007
LRGUK 12.12 2.058e-28 4.11e-24 0.8229
LOC285548 13.16 2.214e-28 4.42e-24 0.8034
ZNF586 11.82 3.232e-27 6.45e-23 0.7562
FLJ45983 11.97 5.249e-27 1.05e-22 0.7522
GATA3 11.97 5.249e-27 1.05e-22 0.7522
ST3GAL1 11.9 9.128e-27 1.82e-22 0.7043

Figure S6.  Get High-res Image As an example, this figure shows the association of INHA__1 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 1.16e-39 with T-test analysis.

Clinical variable #7: 'DISTANT.METASTASIS'

284 genes related to 'DISTANT.METASTASIS'.

Table S13.  Basic characteristics of clinical feature: 'DISTANT.METASTASIS'

DISTANT.METASTASIS Labels N
  M0 246
  M1 36
  M1A 8
  M1B 1
  MX 50
     
  Significant markers N = 284
List of top 10 genes differentially expressed by 'DISTANT.METASTASIS'

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

ANOVA_P Q
JOSD2 5.108e-261 1.02e-256
FAM86B2 1.71e-118 3.41e-114
KCNK4 1.397e-91 2.79e-87
DMKN 1.026e-87 2.05e-83
FZD3 1.169e-70 2.33e-66
LYSMD2 9.041e-67 1.8e-62
TMOD2 9.041e-67 1.8e-62
ETV5 2.557e-64 5.1e-60
FAHD2B 1.002e-53 2e-49
RRM1 2.295e-53 4.58e-49

Figure S7.  Get High-res Image As an example, this figure shows the association of JOSD2 to 'DISTANT.METASTASIS'. P value = 5.11e-261 with ANOVA analysis.

Clinical variable #8: 'LYMPH.NODE.METASTASIS'

14 genes related to 'LYMPH.NODE.METASTASIS'.

Table S15.  Basic characteristics of clinical feature: 'LYMPH.NODE.METASTASIS'

LYMPH.NODE.METASTASIS Labels N
  N0 192
  N1 59
  N1A 16
  N1B 16
  N1C 3
  N2 37
  N2A 5
  N2B 16
  NX 3
     
  Significant markers N = 14
List of top 10 genes differentially expressed by 'LYMPH.NODE.METASTASIS'

Table S16.  Get Full Table List of top 10 genes differentially expressed by 'LYMPH.NODE.METASTASIS'

ANOVA_P Q
LLPH 2.151e-22 4.29e-18
ATP5G3 4.384e-16 8.75e-12
ZNF354A 7.602e-16 1.52e-11
APC 6.757e-12 1.35e-07
LRRC37B2 8.63e-12 1.72e-07
ASTN2 1.312e-11 2.62e-07
TRIM32 1.312e-11 2.62e-07
SCG5 2.162e-08 0.000431
UBE2L6 1.667e-07 0.00333
CCDC50__1 1.734e-07 0.00346

Figure S8.  Get High-res Image As an example, this figure shows the association of LLPH to 'LYMPH.NODE.METASTASIS'. P value = 2.15e-22 with ANOVA analysis.

Clinical variable #9: 'COMPLETENESS.OF.RESECTION'

75 genes related to 'COMPLETENESS.OF.RESECTION'.

Table S17.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 219
  R1 4
  R2 6
  RX 24
     
  Significant markers N = 75
List of top 10 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S18.  Get Full Table List of top 10 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

ANOVA_P Q
UBE2D4 2.92e-16 5.83e-12
URGCP__1 2.92e-16 5.83e-12
TMEM115 1.644e-15 3.28e-11
GGCT 2.76e-12 5.51e-08
EIF5A 5.05e-12 1.01e-07
CD300LF 9.982e-12 1.99e-07
RAB37__1 9.982e-12 1.99e-07
MYD88 2.683e-11 5.35e-07
ZFP14 2.107e-10 4.2e-06
CAPNS2 5.747e-10 1.15e-05

Figure S9.  Get High-res Image As an example, this figure shows the association of UBE2D4 to 'COMPLETENESS.OF.RESECTION'. P value = 2.92e-16 with ANOVA analysis.

Clinical variable #10: 'NUMBER.OF.LYMPH.NODES'

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

Table S19.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 2.23 (4.9)
  Significant markers N = 9
  pos. correlated 9
  neg. correlated 0
List of 9 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

Table S20.  Get Full Table List of 9 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
UBE2L6 0.3554 8.806e-11 1.76e-06
CASP1__1 0.3518 1.398e-10 2.79e-06
IL12RB1 0.2976 7.636e-08 0.00152
SP140L 0.269 1.315e-06 0.0262
MAST3 0.2681 1.436e-06 0.0287
ACTA2__1 0.2666 1.649e-06 0.0329
FAS 0.2666 1.649e-06 0.0329
CASP5 0.2664 1.674e-06 0.0334
MARCH8 0.2653 1.853e-06 0.037

Figure S10.  Get High-res Image As an example, this figure shows the association of UBE2L6 to 'NUMBER.OF.LYMPH.NODES'. P value = 8.81e-11 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #11: 'NEOPLASM.DISEASESTAGE'

465 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S21.  Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 48
  STAGE IA 1
  STAGE II 25
  STAGE IIA 93
  STAGE IIB 6
  STAGE IIC 3
  STAGE III 12
  STAGE IIIA 19
  STAGE IIIB 48
  STAGE IIIC 27
  STAGE IV 24
  STAGE IVA 24
  STAGE IVB 1
     
  Significant markers N = 465
List of top 10 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

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

ANOVA_P Q
JOSD2 3.007e-244 6e-240
FAM86B2 7.272e-108 1.45e-103
KCNK4 5.955e-83 1.19e-78
DMKN 1.468e-73 2.93e-69
FZD3 3.573e-62 7.13e-58
LYSMD2 8.079e-58 1.61e-53
TMOD2 8.079e-58 1.61e-53
ETV5 2.067e-54 4.12e-50
GBP5 2.31e-53 4.61e-49
FAHD2B 1.217e-52 2.43e-48

Figure S11.  Get High-res Image As an example, this figure shows the association of JOSD2 to 'NEOPLASM.DISEASESTAGE'. P value = 3.01e-244 with ANOVA analysis.

Methods & Data
Input
  • Expresson data file = COADREAD-TP.meth.by_min_expr_corr.data.txt

  • Clinical data file = COADREAD-TP.clin.merged.picked.txt

  • Number of patients = 350

  • Number of genes = 19957

  • Number of clinical features = 11

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

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

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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[4] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[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)