Correlation between gene methylation status and clinical features
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 17313 genes and 10 clinical features across 33 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.

  • 239 genes correlated to 'HISTOLOGICAL.TYPE'.

    • LOC100302640 ,  LIMS2 ,  PPP2R3A ,  BEST2 ,  ZNF830 ,  ...

  • 1 gene correlated to 'NUMBERPACKYEARSSMOKED'.

    • PNKP

  • 2 genes correlated to 'TOBACCOSMOKINGHISTORYINDICATOR'.

    • LIG4 ,  PCBD1

  • No genes correlated to 'Time to Death', 'AGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'STOPPEDSMOKINGYEAR', 'DISTANT.METASTASIS', 'LYMPH.NODE.METASTASIS', and 'NUMBER.OF.LYMPH.NODES'.

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=0        
AGE Spearman correlation test   N=0        
HISTOLOGICAL TYPE ANOVA test N=239        
RADIATIONS RADIATION REGIMENINDICATION t test   N=0        
NUMBERPACKYEARSSMOKED Spearman correlation test N=1 higher numberpackyearssmoked N=0 lower numberpackyearssmoked N=1
STOPPEDSMOKINGYEAR Spearman correlation test   N=0        
TOBACCOSMOKINGHISTORYINDICATOR Spearman correlation test N=2 higher tobaccosmokinghistoryindicator N=2 lower tobaccosmokinghistoryindicator N=0
DISTANT METASTASIS t test   N=0        
LYMPH NODE METASTASIS t test   N=0        
NUMBER OF LYMPH NODES Spearman correlation test   N=0        
Clinical variable #1: 'Time to Death'

No gene related to 'Time to Death'.

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

Time to Death Duration (Months) 0.1-101.8 (median=5.7)
  censored N = 25
  death N = 7
     
  Significant markers N = 0
Clinical variable #2: 'AGE'

No gene related to 'AGE'.

Table S2.  Basic characteristics of clinical feature: 'AGE'

AGE Mean (SD) 47.76 (12)
  Significant markers N = 0
Clinical variable #3: 'HISTOLOGICAL.TYPE'

239 genes related to 'HISTOLOGICAL.TYPE'.

Table S3.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  CERVICAL SQUAMOUS CELL CARCINOMA 28
  ENDOCERVICAL TYPE OF ADENOCARCINOMA 1
  SQUAMOUS CELL CARCINOMA 4
     
  Significant markers N = 239
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S4.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
LOC100302640 1.307e-57 2.26e-53
LIMS2 4.099e-55 7.1e-51
PPP2R3A 4.313e-54 7.47e-50
BEST2 6.492e-45 1.12e-40
ZNF830 3.553e-44 6.15e-40
SMARCD3 6.837e-44 1.18e-39
CTU1 5.546e-43 9.6e-39
MTX3 1.556e-40 2.69e-36
GABBR1 1.027e-36 1.78e-32
KLHL10 2.845e-35 4.92e-31

Figure S1.  Get High-res Image As an example, this figure shows the association of LOC100302640 to 'HISTOLOGICAL.TYPE'. P value = 1.31e-57 with ANOVA analysis.

Clinical variable #4: 'RADIATIONS.RADIATION.REGIMENINDICATION'

No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S5.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 12
  YES 21
     
  Significant markers N = 0
Clinical variable #5: 'NUMBERPACKYEARSSMOKED'

One gene related to 'NUMBERPACKYEARSSMOKED'.

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

NUMBERPACKYEARSSMOKED Mean (SD) 18.67 (12)
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one gene significantly correlated to 'NUMBERPACKYEARSSMOKED' by Spearman correlation test

Table S7.  Get Full Table List of one gene significantly correlated to 'NUMBERPACKYEARSSMOKED' by Spearman correlation test

SpearmanCorr corrP Q
PNKP -0.9958 1.542e-08 0.000267

Figure S2.  Get High-res Image As an example, this figure shows the association of PNKP to 'NUMBERPACKYEARSSMOKED'. P value = 1.54e-08 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #6: 'STOPPEDSMOKINGYEAR'

No gene related to 'STOPPEDSMOKINGYEAR'.

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

STOPPEDSMOKINGYEAR Mean (SD) 1994.67 (17)
  Value N
  1978 1
  1995 1
  2011 1
     
  Significant markers N = 0
Clinical variable #7: 'TOBACCOSMOKINGHISTORYINDICATOR'

2 genes related to 'TOBACCOSMOKINGHISTORYINDICATOR'.

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

TOBACCOSMOKINGHISTORYINDICATOR Mean (SD) 1.87 (1.1)
  Value N
  1 15
  2 9
  3 1
  4 5
     
  Significant markers N = 2
  pos. correlated 2
  neg. correlated 0
List of 2 genes significantly correlated to 'TOBACCOSMOKINGHISTORYINDICATOR' by Spearman correlation test

Table S10.  Get Full Table List of 2 genes significantly correlated to 'TOBACCOSMOKINGHISTORYINDICATOR' by Spearman correlation test

SpearmanCorr corrP Q
LIG4 0.7561 1.347e-06 0.0233
PCBD1 0.7537 1.522e-06 0.0263

Figure S3.  Get High-res Image As an example, this figure shows the association of LIG4 to 'TOBACCOSMOKINGHISTORYINDICATOR'. P value = 1.35e-06 with Spearman correlation analysis.

Clinical variable #8: 'DISTANT.METASTASIS'

No gene related to 'DISTANT.METASTASIS'.

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

DISTANT.METASTASIS Labels N
  M0 21
  MX 7
     
  Significant markers N = 0
Clinical variable #9: 'LYMPH.NODE.METASTASIS'

No gene related to 'LYMPH.NODE.METASTASIS'.

Table S12.  Basic characteristics of clinical feature: 'LYMPH.NODE.METASTASIS'

LYMPH.NODE.METASTASIS Labels N
  N0 18
  N1 11
     
  Significant markers N = 0
Clinical variable #10: 'NUMBER.OF.LYMPH.NODES'

No gene related to 'NUMBER.OF.LYMPH.NODES'.

Table S13.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 1.03 (3)
  Value N
  0 19
  1 6
  2 2
  4 1
  16 1
     
  Significant markers N = 0
Methods & Data
Input

  • Expresson data file = CESC-TP.meth.for_correlation.filtered_data.txt

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

  • Number of patients = 33

  • Number of genes = 17313

  • Number of clinical features = 10

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

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

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

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.

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