Correlation between gene methylation status and clinical features
Breast Invasive Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C16W982H
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/C16W982H
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 19950 genes and 9 clinical features across 575 samples, statistically thresholded by Q value < 0.05, 9 clinical features related to at least one genes.

  • 6 genes correlated to 'Time to Death'.

    • MTHFD1 ,  CDC73 ,  MIR1278 ,  PIH1D1 ,  ALDH16A1 ,  ...

  • 197 genes correlated to 'AGE'.

    • KIAA1143 ,  KIF15 ,  C1ORF103 ,  LGALS8 ,  C10ORF35 ,  ...

  • 193 genes correlated to 'GENDER'.

    • ALDOC ,  ZNF486 ,  C19ORF24 ,  CIRBP__2 ,  DNAJC15 ,  ...

  • 448 genes correlated to 'HISTOLOGICAL.TYPE'.

    • ZNF230 ,  ZNF846 ,  JOSD2 ,  GTF2F1 ,  LOC100288730 ,  ...

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

    • TUBA4A ,  TUBA4B ,  NDUFB4 ,  SNRPF ,  TBCA ,  ...

  • 21 genes correlated to 'DISTANT.METASTASIS'.

    • RHBDL3 ,  MMAB ,  MVK ,  NHEDC1 ,  SAG ,  ...

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

    • SS18L1__1 ,  ZNF235 ,  MANBAL ,  TPCN2 ,  ZNF33A ,  ...

  • 1 gene correlated to 'NUMBER.OF.LYMPH.NODES'.

    • TCP11L1

  • 40 genes correlated to 'NEOPLASM.DISEASESTAGE'.

    • IDH3B ,  TMX4 ,  DRG2 ,  HIST1H4C ,  WDR74 ,  ...

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=6 shorter survival N=4 longer survival N=2
AGE Spearman correlation test N=197 older N=181 younger N=16
GENDER t test N=193 male N=50 female N=143
HISTOLOGICAL TYPE ANOVA test N=448        
RADIATIONS RADIATION REGIMENINDICATION t test N=204 yes N=164 no N=40
DISTANT METASTASIS ANOVA test N=21        
LYMPH NODE METASTASIS ANOVA test N=76        
NUMBER OF LYMPH NODES Spearman correlation test N=1 higher number.of.lymph.nodes N=1 lower number.of.lymph.nodes N=0
NEOPLASM DISEASESTAGE ANOVA test N=40        
Clinical variable #1: 'Time to Death'

6 genes related to 'Time to Death'.

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

Time to Death Duration (Months) 0-223.4 (median=17.7)
  censored N = 485
  death N = 61
     
  Significant markers N = 6
  associated with shorter survival 4
  associated with longer survival 2
List of 6 genes significantly associated with 'Time to Death' by Cox regression test

Table S2.  Get Full Table List of 6 genes significantly associated with 'Time to Death' by Cox regression test

HazardRatio Wald_P Q C_index
MTHFD1 5000000001 1.749e-08 0.00035 0.655
CDC73 0 1.318e-06 0.026 0.358
MIR1278 0 1.318e-06 0.026 0.358
PIH1D1 141 1.588e-06 0.032 0.545
ALDH16A1 3801 1.878e-06 0.037 0.548
PIH1D1__1 3801 1.878e-06 0.037 0.548

Figure S1.  Get High-res Image As an example, this figure shows the association of MTHFD1 to 'Time to Death'. four curves present the cumulative survival rates of 4 quartile subsets of patients. P value = 1.75e-08 with univariate Cox regression analysis using continuous log-2 expression values.

Clinical variable #2: 'AGE'

197 genes related to 'AGE'.

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

AGE Mean (SD) 57.87 (13)
  Significant markers N = 197
  pos. correlated 181
  neg. correlated 16
List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

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

SpearmanCorr corrP Q
KIAA1143 0.3254 1.277e-15 2.55e-11
KIF15 0.3254 1.277e-15 2.55e-11
C1ORF103 0.3154 1.017e-14 2.03e-10
LGALS8 -0.2851 3.4e-12 6.78e-08
C10ORF35 0.2817 6.203e-12 1.24e-07
EGR2 0.281 7.116e-12 1.42e-07
MEX3C 0.2791 9.842e-12 1.96e-07
CACNA2D1 0.2782 1.167e-11 2.33e-07
BMPER 0.2736 2.575e-11 5.13e-07
RPS2__2 0.2722 3.273e-11 6.53e-07

Figure S2.  Get High-res Image As an example, this figure shows the association of KIAA1143 to 'AGE'. P value = 1.28e-15 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'GENDER'

193 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 569
  MALE 6
     
  Significant markers N = 193
  Higher in MALE 50
  Higher in FEMALE 143
List of top 10 genes differentially expressed by 'GENDER'

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

T(pos if higher in 'MALE') ttestP Q AUC
ALDOC -27.01 8.262e-102 1.65e-97 0.872
ZNF486 -19.2 1.713e-63 3.42e-59 0.8207
C19ORF24 18.66 9.298e-61 1.85e-56 0.8225
CIRBP__2 18.66 9.298e-61 1.85e-56 0.8225
DNAJC15 -14.13 4.057e-37 8.09e-33 0.7299
NMNAT3 -13.71 2.479e-36 4.94e-32 0.6977
LOC400043 -13.49 5.046e-32 1.01e-27 0.5971
EML1 -11.89 5.384e-29 1.07e-24 0.609
RND2 -13.34 3.968e-28 7.91e-24 0.7912
SPC25 -12.84 1.122e-27 2.24e-23 0.754

Figure S3.  Get High-res Image As an example, this figure shows the association of ALDOC to 'GENDER'. P value = 8.26e-102 with T-test analysis.

Clinical variable #4: 'HISTOLOGICAL.TYPE'

448 genes related to 'HISTOLOGICAL.TYPE'.

Table S7.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  INFILTRATING DUCTAL CARCINOMA 420
  INFILTRATING LOBULAR CARCINOMA 95
  MEDULLARY CARCINOMA 4
  MIXED HISTOLOGY (PLEASE SPECIFY) 21
  MUCINOUS CARCINOMA 8
  OTHER SPECIFY 27
     
  Significant markers N = 448
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S8.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
ZNF230 2.339e-28 4.67e-24
ZNF846 9.051e-24 1.81e-19
JOSD2 1.319e-17 2.63e-13
GTF2F1 6.828e-16 1.36e-11
LOC100288730 7.101e-16 1.42e-11
PAN3 7.101e-16 1.42e-11
TAT 1.092e-15 2.18e-11
FN1 1.142e-14 2.28e-10
TNK2 3.016e-14 6.01e-10
GADD45B 5.269e-14 1.05e-09

Figure S4.  Get High-res Image As an example, this figure shows the association of ZNF230 to 'HISTOLOGICAL.TYPE'. P value = 2.34e-28 with ANOVA analysis.

Clinical variable #5: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

Table S9.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 147
  YES 428
     
  Significant markers N = 204
  Higher in YES 164
  Higher in NO 40
List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S10.  Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

T(pos if higher in 'YES') ttestP Q AUC
TUBA4A 6.86 2.539e-11 5.07e-07 0.6536
TUBA4B 6.86 2.539e-11 5.07e-07 0.6536
NDUFB4 6.73 8.652e-11 1.73e-06 0.6685
SNRPF 6.64 1.129e-10 2.25e-06 0.6555
TBCA 6.59 1.488e-10 2.97e-06 0.6524
NECAP1 6.58 1.748e-10 3.49e-06 0.655
C12ORF52__1 6.57 2.063e-10 4.12e-06 0.6606
DDX54 6.57 2.063e-10 4.12e-06 0.6606
TICAM1 6.55 2.471e-10 4.93e-06 0.6665
HDGF 6.33 7.247e-10 1.45e-05 0.6346

Figure S5.  Get High-res Image As an example, this figure shows the association of TUBA4A to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 2.54e-11 with T-test analysis.

Clinical variable #6: 'DISTANT.METASTASIS'

21 genes related to 'DISTANT.METASTASIS'.

Table S11.  Basic characteristics of clinical feature: 'DISTANT.METASTASIS'

DISTANT.METASTASIS Labels N
  CM0 (I+) 1
  M0 491
  M1 6
  MX 77
     
  Significant markers N = 21
List of top 10 genes differentially expressed by 'DISTANT.METASTASIS'

Table S12.  Get Full Table List of top 10 genes differentially expressed by 'DISTANT.METASTASIS'

ANOVA_P Q
RHBDL3 1.438e-22 2.87e-18
MMAB 6.135e-20 1.22e-15
MVK 6.135e-20 1.22e-15
NHEDC1 4.245e-18 8.47e-14
SAG 1.073e-11 2.14e-07
PACRGL 9.222e-11 1.84e-06
C9ORF153 1.743e-08 0.000348
TRIM21 3.719e-08 0.000742
LARS 5.951e-08 0.00119
AK1 7.499e-08 0.0015

Figure S6.  Get High-res Image As an example, this figure shows the association of RHBDL3 to 'DISTANT.METASTASIS'. P value = 1.44e-22 with ANOVA analysis.

Clinical variable #7: 'LYMPH.NODE.METASTASIS'

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

Table S13.  Basic characteristics of clinical feature: 'LYMPH.NODE.METASTASIS'

LYMPH.NODE.METASTASIS Labels N
  N0 157
  N0 (I+) 14
  N0 (I-) 81
  N0 (MOL+) 1
  N1 74
  N1A 87
  N1B 23
  N1C 2
  N1MI 15
  N2 38
  N2A 43
  N3 13
  N3A 18
  N3B 2
  NX 7
     
  Significant markers N = 76
List of top 10 genes differentially expressed by 'LYMPH.NODE.METASTASIS'

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

ANOVA_P Q
SS18L1__1 1.012e-76 2.02e-72
ZNF235 8.102e-55 1.62e-50
MANBAL 4.687e-23 9.35e-19
TPCN2 7.296e-19 1.46e-14
ZNF33A 6.593e-14 1.32e-09
CLPP 2.202e-11 4.39e-07
LRRC29 2.859e-11 5.7e-07
TMEM208 2.859e-11 5.7e-07
KCNQ5 8.408e-11 1.68e-06
RG9MTD1 1.84e-10 3.67e-06

Figure S7.  Get High-res Image As an example, this figure shows the association of SS18L1__1 to 'LYMPH.NODE.METASTASIS'. P value = 1.01e-76 with ANOVA analysis.

Clinical variable #8: 'NUMBER.OF.LYMPH.NODES'

One gene related to 'NUMBER.OF.LYMPH.NODES'.

Table S15.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 2.46 (4.6)
  Significant markers N = 1
  pos. correlated 1
  neg. correlated 0
List of one gene significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

Table S16.  Get Full Table List of one gene significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
TCP11L1 0.2122 7.435e-07 0.0148

Figure S8.  Get High-res Image As an example, this figure shows the association of TCP11L1 to 'NUMBER.OF.LYMPH.NODES'. P value = 7.43e-07 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #9: 'NEOPLASM.DISEASESTAGE'

40 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S17.  Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 45
  STAGE IA 45
  STAGE IB 2
  STAGE II 8
  STAGE IIA 185
  STAGE IIB 131
  STAGE III 2
  STAGE IIIA 99
  STAGE IIIB 16
  STAGE IIIC 30
  STAGE IV 6
  STAGE X 5
     
  Significant markers N = 40
List of top 10 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

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

ANOVA_P Q
IDH3B 1.961e-71 3.91e-67
TMX4 9.656e-58 1.93e-53
DRG2 5.338e-32 1.06e-27
HIST1H4C 3.88e-20 7.74e-16
WDR74 2.603e-18 5.19e-14
RHBDL3 1.252e-17 2.5e-13
ATP5J 1.388e-15 2.77e-11
GABPA 1.388e-15 2.77e-11
LNP1 2.501e-15 4.99e-11
TOMM70A 2.501e-15 4.99e-11

Figure S9.  Get High-res Image As an example, this figure shows the association of IDH3B to 'NEOPLASM.DISEASESTAGE'. P value = 1.96e-71 with ANOVA analysis.

Methods & Data
Input

  • Expresson data file = BRCA-TP.meth.by_min_expr_corr.data.txt

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

  • Number of patients = 575

  • Number of genes = 19950

  • Number of clinical features = 9

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)
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