Correlation between gene methylation status and clinical features
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C10V8BMX
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene methylation status and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C10V8BMX
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 19971 genes and 45 clinical features across 243 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 17 clinical features related to at least one genes.

  • 33 genes correlated to 'AGE'.

    • RARB ,  OAZ2 ,  CHRNB1 ,  SP4 ,  EYA4 ,  ...

  • 2188 genes correlated to 'HISTOLOGICAL.TYPE'.

    • ATP10D ,  TMEM117 ,  DST ,  C10ORF108 ,  DIP2C__1 ,  ...

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

    • CDKN2AIPNL ,  HIST1H1E ,  AGPAT3 ,  CLEC2L ,  CEP97 ,  ...

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

    • RCAN1 ,  NUAK1

  • 1 gene correlated to 'RACE'.

    • SNX16

  • 2 genes correlated to 'WEIGHT_KG_AT_DIAGNOSIS'.

    • RUVBL1 ,  ACAD9

  • 150 genes correlated to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.

    • MAN2B1 ,  MORG1__1 ,  HDHD3 ,  HCN2 ,  ANKRD52 ,  ...

  • 4 genes correlated to 'NEOPLASMHISTOLOGICGRADE'.

    • GMNN ,  MTF2 ,  BRIX1 ,  RAD1

  • 1 gene correlated to 'RADIATION_TOTAL_DOSE'.

    • MBTPS1

  • 145 genes correlated to 'RADIATION_THERAPY_TYPE'.

    • HIST1H1E ,  CDKN2AIPNL ,  PRPF6 ,  DNLZ ,  RSPH3 ,  ...

  • 18 genes correlated to 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.

    • ANKS1A ,  TAF3 ,  POLR2D ,  ZNF592 ,  KNTC1 ,  ...

  • 9 genes correlated to 'MENOPAUSE_STATUS'.

    • C21ORF34 ,  MIR99A ,  MIRLET7C ,  RARB ,  SSBP3 ,  ...

  • 3 genes correlated to 'LYMPHOVASCULAR_INVOLVEMENT'.

    • ZNF445 ,  MKRN2 ,  TMEM87B

  • 2 genes correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

    • RCAN1 ,  NUAK1

  • 221 genes correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.

    • EBNA1BP2__1 ,  WDR65__1 ,  MMD ,  C21ORF57 ,  HIST2H2AB ,  ...

  • 2 genes correlated to 'CERVIX_SUV_RESULTS'.

    • C11ORF87 ,  MRPL28

  • 30 genes correlated to 'AGE_AT_DIAGNOSIS'.

    • RARB ,  OAZ2 ,  CHRNB1 ,  CDIPT ,  LOC440356 ,  ...

  • No genes correlated to 'Time to Death', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'NUMBERPACKYEARSSMOKED', 'ETHNICITY', 'TUMOR_STATUS', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_PACK_YEARS_SMOKED', 'TOBACCO_SMOKING_HISTORY', 'PATIENT.AGEBEGANSMOKINGINYEARS', 'RADIATION_THERAPY_STATUS', 'RADIATION_THERAPY_SITE', 'RADIATION_ADJUVANT_UNITS', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PREGNANCIES_COUNT_LIVE_BIRTH', 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT', 'PREGNANCIES_COUNT_ECTOPIC', 'POS_LYMPH_NODE_LOCATION', 'LYMPH_NODES_EXAMINED', 'KERATINIZATION_SQUAMOUS_CELL', 'HISTORY_HORMONAL_CONTRACEPTIVES_USE', 'HEIGHT_CM_AT_DIAGNOSIS', 'CORPUS_INVOLVEMENT', 'CHEMO_CONCURRENT_TYPE', 'AJCC_TUMOR_PATHOLOGIC_PT', and 'STAGE_EVENT.CLINICAL_STAGE'.

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
Time to Death Cox regression test   N=0        
AGE Spearman correlation test N=33 older N=9 younger N=24
PATHOLOGY T STAGE Spearman correlation test   N=0        
PATHOLOGY N STAGE Wilcoxon test   N=0        
PATHOLOGY M STAGE Kruskal-Wallis test   N=0        
HISTOLOGICAL TYPE Kruskal-Wallis test N=2188        
RADIATIONS RADIATION REGIMENINDICATION Wilcoxon test N=276 yes N=276 no N=0
NUMBERPACKYEARSSMOKED Spearman correlation test   N=0        
NUMBER OF LYMPH NODES Spearman correlation test N=2 higher number.of.lymph.nodes N=2 lower number.of.lymph.nodes N=0
RACE Kruskal-Wallis test N=1        
ETHNICITY Wilcoxon test   N=0        
WEIGHT_KG_AT_DIAGNOSIS Spearman correlation test N=2 higher weight_kg_at_diagnosis N=2 lower weight_kg_at_diagnosis N=0
TUMOR_STATUS Wilcoxon test   N=0        
TUMOR_SAMPLE_PROCUREMENT_COUNTRY Kruskal-Wallis test N=150        
NEOPLASMHISTOLOGICGRADE Kruskal-Wallis test N=4        
TOBACCO_SMOKING_YEAR_STOPPED Spearman correlation test   N=0        
TOBACCO_SMOKING_PACK_YEARS_SMOKED Spearman correlation test   N=0        
TOBACCO_SMOKING_HISTORY Kruskal-Wallis test   N=0        
PATIENT AGEBEGANSMOKINGINYEARS Spearman correlation test   N=0        
RADIATION_TOTAL_DOSE Spearman correlation test N=1 higher radiation_total_dose N=1 lower radiation_total_dose N=0
RADIATION_THERAPY_TYPE Kruskal-Wallis test N=145        
RADIATION_THERAPY_STATUS Wilcoxon test   N=0        
RADIATION_THERAPY_SITE Kruskal-Wallis test   N=0        
RADIATION_ADJUVANT_UNITS Wilcoxon test   N=0        
PREGNANCIES_COUNT_TOTAL Spearman correlation test   N=0        
PREGNANCIES_COUNT_STILLBIRTH Spearman correlation test   N=0        
PATIENT PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT Spearman correlation test N=18 higher patient.patientpregnancyspontaneousabortioncount N=12 lower patient.patientpregnancyspontaneousabortioncount N=6
PREGNANCIES_COUNT_LIVE_BIRTH Spearman correlation test   N=0        
PATIENT PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT Spearman correlation test   N=0        
PREGNANCIES_COUNT_ECTOPIC Spearman correlation test   N=0        
POS_LYMPH_NODE_LOCATION Kruskal-Wallis test   N=0        
MENOPAUSE_STATUS Kruskal-Wallis test N=9        
LYMPHOVASCULAR_INVOLVEMENT Wilcoxon test N=3 present N=3 absent N=0
LYMPH_NODES_EXAMINED_HE_COUNT Spearman correlation test N=2 higher lymph_nodes_examined_he_count N=2 lower lymph_nodes_examined_he_count N=0
LYMPH_NODES_EXAMINED Spearman correlation test   N=0        
KERATINIZATION_SQUAMOUS_CELL Wilcoxon test   N=0        
INITIAL_PATHOLOGIC_DX_YEAR Spearman correlation test N=221 higher initial_pathologic_dx_year N=5 lower initial_pathologic_dx_year N=216
HISTORY_HORMONAL_CONTRACEPTIVES_USE Kruskal-Wallis test   N=0        
HEIGHT_CM_AT_DIAGNOSIS Spearman correlation test   N=0        
CORPUS_INVOLVEMENT Wilcoxon test   N=0        
CHEMO_CONCURRENT_TYPE Kruskal-Wallis test   N=0        
CERVIX_SUV_RESULTS Spearman correlation test N=2 higher cervix_suv_results N=0 lower cervix_suv_results N=2
AJCC_TUMOR_PATHOLOGIC_PT Kruskal-Wallis test   N=0        
AGE_AT_DIAGNOSIS Spearman correlation test N=30 higher age_at_diagnosis N=9 lower age_at_diagnosis N=21
STAGE_EVENT CLINICAL_STAGE Kruskal-Wallis 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) 0-195.8 (median=15.9)
  censored N = 185
  death N = 53
     
  Significant markers N = 0
Clinical variable #2: 'AGE'

33 genes related to 'AGE'.

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

AGE Mean (SD) 47.38 (14)
  Significant markers N = 33
  pos. correlated 9
  neg. correlated 24
List of top 10 genes differentially expressed by 'AGE'

Table S3.  Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
RARB -0.368 4.436e-09 8.86e-05
OAZ2 -0.3355 1.066e-07 0.00213
CHRNB1 0.3288 1.97e-07 0.00393
SP4 -0.3093 1.08e-06 0.0216
EYA4 0.3085 1.153e-06 0.023
CDIPT -0.3003 2.265e-06 0.0452
LOC440356 -0.3003 2.265e-06 0.0452
CD9 -0.3002 2.284e-06 0.0456
HMGCS1 -0.2982 2.701e-06 0.0539
RHOF 0.2955 3.341e-06 0.0667
Clinical variable #3: 'PATHOLOGY.T.STAGE'

No gene related to 'PATHOLOGY.T.STAGE'.

Table S4.  Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE Mean (SD) 1.41 (0.68)
  N
  1 125
  2 48
  3 8
  4 4
     
  Significant markers N = 0
Clinical variable #4: 'PATHOLOGY.N.STAGE'

No gene related to 'PATHOLOGY.N.STAGE'.

Table S5.  Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'

PATHOLOGY.N.STAGE Labels N
  class0 115
  class1 50
     
  Significant markers N = 0
Clinical variable #5: 'PATHOLOGY.M.STAGE'

No gene related to 'PATHOLOGY.M.STAGE'.

Table S6.  Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE Labels N
  M0 99
  M1 8
  MX 89
     
  Significant markers N = 0
Clinical variable #6: 'HISTOLOGICAL.TYPE'

2188 genes related to 'HISTOLOGICAL.TYPE'.

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

HISTOLOGICAL.TYPE Labels N
  ADENOSQUAMOUS 4
  CERVICAL SQUAMOUS CELL CARCINOMA 204
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA 22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE 6
     
  Significant markers N = 2188
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
ATP10D 1.076e-16 2.15e-12
TMEM117 2.849e-16 5.69e-12
DST 1.225e-15 2.45e-11
C10ORF108 1.587e-15 3.17e-11
DIP2C__1 1.587e-15 3.17e-11
RGS12 1.874e-15 3.74e-11
BICD2 1.951e-15 3.9e-11
CTBP2 2.573e-15 5.14e-11
AKR1B10 2.581e-15 5.15e-11
CLDN3 3.212e-15 6.41e-11
Clinical variable #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

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

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 35
  YES 208
     
  Significant markers N = 276
  Higher in YES 276
  Higher in NO 0
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'

W(pos if higher in 'YES') wilcoxontestP Q AUC
CDKN2AIPNL 1132 7.156e-11 1.43e-06 0.8445
HIST1H1E 6088 1.999e-10 3.99e-06 0.8363
AGPAT3 1283 9.075e-10 1.81e-05 0.8238
CLEC2L 1301 1.216e-09 2.43e-05 0.8213
CEP97 1338 2.205e-09 4.4e-05 0.8162
C22ORF30 1359 3.079e-09 6.15e-05 0.8133
DNLZ 1362 3.228e-09 6.45e-05 0.8129
RSPH3 1380 4.286e-09 8.56e-05 0.8104
C22ORF26 1382 4.422e-09 8.83e-05 0.8102
LOC150381 1382 4.422e-09 8.83e-05 0.8102
Clinical variable #8: 'NUMBERPACKYEARSSMOKED'

No gene related to 'NUMBERPACKYEARSSMOKED'.

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

NUMBERPACKYEARSSMOKED Mean (SD) 18.37 (13)
  Significant markers N = 0
Clinical variable #9: 'NUMBER.OF.LYMPH.NODES'

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

Table S12.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 1.04 (2.4)
  Significant markers N = 2
  pos. correlated 2
  neg. correlated 0
List of 2 genes differentially expressed by 'NUMBER.OF.LYMPH.NODES'

Table S13.  Get Full Table List of 2 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
RCAN1 0.4235 1.515e-07 0.00303
NUAK1 0.3779 3.547e-06 0.0708
Clinical variable #10: 'RACE'

One gene related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 8
  ASIAN 19
  BLACK OR AFRICAN AMERICAN 26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 1
  WHITE 172
     
  Significant markers N = 1
List of one gene differentially expressed by 'RACE'

Table S15.  Get Full Table List of one gene differentially expressed by 'RACE'

ANOVA_P Q
SNX16 4.358e-06 0.087
Clinical variable #11: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 17
  NOT HISPANIC OR LATINO 155
     
  Significant markers N = 0
Clinical variable #12: 'WEIGHT_KG_AT_DIAGNOSIS'

2 genes related to 'WEIGHT_KG_AT_DIAGNOSIS'.

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

WEIGHT_KG_AT_DIAGNOSIS Mean (SD) 74.96 (23)
  Significant markers N = 2
  pos. correlated 2
  neg. correlated 0
List of 2 genes differentially expressed by 'WEIGHT_KG_AT_DIAGNOSIS'

Table S18.  Get Full Table List of 2 genes significantly correlated to 'WEIGHT_KG_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
RUVBL1 0.2923 1e-05 0.2
ACAD9 0.2887 1.295e-05 0.259
Clinical variable #13: 'TUMOR_STATUS'

No gene related to 'TUMOR_STATUS'.

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

TUMOR_STATUS Labels N
  TUMOR FREE 75
  WITH TUMOR 28
     
  Significant markers N = 0
Clinical variable #14: 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

150 genes related to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.

Table S20.  Basic characteristics of clinical feature: 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

TUMOR_SAMPLE_PROCUREMENT_COUNTRY Labels N
  BRAZIL 20
  CANADA 5
  NIGERIA 1
  RUSSIA 11
  UKRAINE 7
  UNITED STATES 185
  VIETNAM 14
     
  Significant markers N = 150
List of top 10 genes differentially expressed by 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

Table S21.  Get Full Table List of top 10 genes differentially expressed by 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

ANOVA_P Q
MAN2B1 5.93e-10 1.18e-05
MORG1__1 5.93e-10 1.18e-05
HDHD3 1.28e-09 2.56e-05
HCN2 2.873e-09 5.74e-05
ANKRD52 1.694e-08 0.000338
HAX1 2.332e-08 0.000466
LHX4 2.632e-08 0.000525
LRP10 3.132e-08 0.000625
C14ORF21 3.201e-08 0.000639
DHRS1 3.201e-08 0.000639
Clinical variable #15: 'NEOPLASMHISTOLOGICGRADE'

4 genes related to 'NEOPLASMHISTOLOGICGRADE'.

Table S22.  Basic characteristics of clinical feature: 'NEOPLASMHISTOLOGICGRADE'

NEOPLASMHISTOLOGICGRADE Labels N
  G1 15
  G2 112
  G3 98
  G4 1
  GX 14
     
  Significant markers N = 4
List of 4 genes differentially expressed by 'NEOPLASMHISTOLOGICGRADE'

Table S23.  Get Full Table List of 4 genes differentially expressed by 'NEOPLASMHISTOLOGICGRADE'

ANOVA_P Q
GMNN 7.072e-08 0.00141
MTF2 1.773e-06 0.0354
BRIX1 1.095e-05 0.219
RAD1 1.095e-05 0.219
Clinical variable #16: 'TOBACCO_SMOKING_YEAR_STOPPED'

No gene related to 'TOBACCO_SMOKING_YEAR_STOPPED'.

Table S24.  Basic characteristics of clinical feature: 'TOBACCO_SMOKING_YEAR_STOPPED'

TOBACCO_SMOKING_YEAR_STOPPED Mean (SD) 2000.41 (11)
  Significant markers N = 0
Clinical variable #17: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'

No gene related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.

Table S25.  Basic characteristics of clinical feature: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'

TOBACCO_SMOKING_PACK_YEARS_SMOKED Mean (SD) 18.37 (13)
  Significant markers N = 0
Clinical variable #18: 'TOBACCO_SMOKING_HISTORY'

No gene related to 'TOBACCO_SMOKING_HISTORY'.

Table S26.  Basic characteristics of clinical feature: 'TOBACCO_SMOKING_HISTORY'

TOBACCO_SMOKING_HISTORY Labels N
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS 33
  CURRENT REFORMED SMOKER FOR > 15 YEARS 8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED 3
  CURRENT SMOKER 53
  LIFELONG NON-SMOKER 108
     
  Significant markers N = 0
Clinical variable #19: 'PATIENT.AGEBEGANSMOKINGINYEARS'

No gene related to 'PATIENT.AGEBEGANSMOKINGINYEARS'.

Table S27.  Basic characteristics of clinical feature: 'PATIENT.AGEBEGANSMOKINGINYEARS'

PATIENT.AGEBEGANSMOKINGINYEARS Mean (SD) 21.48 (7.9)
  Significant markers N = 0
Clinical variable #20: 'RADIATION_TOTAL_DOSE'

One gene related to 'RADIATION_TOTAL_DOSE'.

Table S28.  Basic characteristics of clinical feature: 'RADIATION_TOTAL_DOSE'

RADIATION_TOTAL_DOSE Mean (SD) 3933.6 (1600)
  Significant markers N = 1
  pos. correlated 1
  neg. correlated 0
List of one gene differentially expressed by 'RADIATION_TOTAL_DOSE'

Table S29.  Get Full Table List of one gene significantly correlated to 'RADIATION_TOTAL_DOSE' by Spearman correlation test

SpearmanCorr corrP Q
MBTPS1 0.4232 7.616e-06 0.152
Clinical variable #21: 'RADIATION_THERAPY_TYPE'

145 genes related to 'RADIATION_THERAPY_TYPE'.

Table S30.  Basic characteristics of clinical feature: 'RADIATION_THERAPY_TYPE'

RADIATION_THERAPY_TYPE Labels N
  COMBINATION 20
  EXTERNAL 72
  EXTERNAL BEAM 15
  IMPLANTS 1
  INTERNAL 11
     
  Significant markers N = 145
List of top 10 genes differentially expressed by 'RADIATION_THERAPY_TYPE'

Table S31.  Get Full Table List of top 10 genes differentially expressed by 'RADIATION_THERAPY_TYPE'

ANOVA_P Q
HIST1H1E 4.979e-10 9.94e-06
CDKN2AIPNL 7.908e-10 1.58e-05
PRPF6 1.261e-09 2.52e-05
DNLZ 3.018e-09 6.03e-05
RSPH3 4.351e-09 8.69e-05
DCDC1__1 7.364e-09 0.000147
DNAJC24__1 7.364e-09 0.000147
C22ORF30 1.373e-08 0.000274
CLEC2L 1.375e-08 0.000274
FAM119B 1.982e-08 0.000396
Clinical variable #22: 'RADIATION_THERAPY_STATUS'

No gene related to 'RADIATION_THERAPY_STATUS'.

Table S32.  Basic characteristics of clinical feature: 'RADIATION_THERAPY_STATUS'

RADIATION_THERAPY_STATUS Labels N
  COMPLETED AS PLANNED 29
  TREATMENT NOT COMPLETED 3
     
  Significant markers N = 0
Clinical variable #23: 'RADIATION_THERAPY_SITE'

No gene related to 'RADIATION_THERAPY_SITE'.

Table S33.  Basic characteristics of clinical feature: 'RADIATION_THERAPY_SITE'

RADIATION_THERAPY_SITE Labels N
  DISTANT RECURRENCE 2
  LOCAL RECURRENCE 2
  PRIMARY TUMOR FIELD 28
  REGIONAL SITE 13
     
  Significant markers N = 0
Clinical variable #24: 'RADIATION_ADJUVANT_UNITS'

No gene related to 'RADIATION_ADJUVANT_UNITS'.

Table S34.  Basic characteristics of clinical feature: 'RADIATION_ADJUVANT_UNITS'

RADIATION_ADJUVANT_UNITS Labels N
  CGY 31
  GY 3
     
  Significant markers N = 0
Clinical variable #25: 'PREGNANCIES_COUNT_TOTAL'

No gene related to 'PREGNANCIES_COUNT_TOTAL'.

Table S35.  Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_TOTAL'

PREGNANCIES_COUNT_TOTAL Mean (SD) 3.55 (2.5)
  Significant markers N = 0
Clinical variable #26: 'PREGNANCIES_COUNT_STILLBIRTH'

No gene related to 'PREGNANCIES_COUNT_STILLBIRTH'.

Table S36.  Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_STILLBIRTH'

PREGNANCIES_COUNT_STILLBIRTH Mean (SD) 0.07 (0.36)
  Value N
  0 101
  1 5
  3 1
     
  Significant markers N = 0
Clinical variable #27: 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

18 genes related to 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.

Table S37.  Basic characteristics of clinical feature: 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT Mean (SD) 0.47 (0.83)
  Significant markers N = 18
  pos. correlated 12
  neg. correlated 6
List of top 10 genes differentially expressed by 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

Table S38.  Get Full Table List of top 10 genes significantly correlated to 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT' by Spearman correlation test

SpearmanCorr corrP Q
ANKS1A 0.4395 1.207e-07 0.00241
TAF3 0.4242 3.615e-07 0.00722
POLR2D 0.4203 4.737e-07 0.00946
ZNF592 -0.4087 1.043e-06 0.0208
KNTC1 0.4035 1.763e-06 0.0352
RSRC2 0.4035 1.763e-06 0.0352
KIR2DS4 0.4007 1.765e-06 0.0352
DPM1__1 0.3914 3.477e-06 0.0694
MOCS3__1 0.3914 3.477e-06 0.0694
WDR67 0.3755 8.439e-06 0.168
Clinical variable #28: 'PREGNANCIES_COUNT_LIVE_BIRTH'

No gene related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

Table S39.  Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_LIVE_BIRTH'

PREGNANCIES_COUNT_LIVE_BIRTH Mean (SD) 2.6 (1.8)
  Significant markers N = 0
Clinical variable #29: 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

No gene related to 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.

Table S40.  Basic characteristics of clinical feature: 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT Mean (SD) 0.86 (1.8)
  Significant markers N = 0
Clinical variable #30: 'PREGNANCIES_COUNT_ECTOPIC'

No gene related to 'PREGNANCIES_COUNT_ECTOPIC'.

Table S41.  Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_ECTOPIC'

PREGNANCIES_COUNT_ECTOPIC Mean (SD) 0.1 (0.33)
  Value N
  0 99
  1 9
  2 1
     
  Significant markers N = 0
Clinical variable #31: 'POS_LYMPH_NODE_LOCATION'

No gene related to 'POS_LYMPH_NODE_LOCATION'.

Table S42.  Basic characteristics of clinical feature: 'POS_LYMPH_NODE_LOCATION'

POS_LYMPH_NODE_LOCATION Labels N
  MACROSCOPIC PARAMETRIAL INVOLVEMENT 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT 7
  OTHER LOCATION, SPECIFY 33
  POSITIVE BLADDER MARGIN 1
  POSITIVE VAGINAL MARGIN 9
     
  Significant markers N = 0
Clinical variable #32: 'MENOPAUSE_STATUS'

9 genes related to 'MENOPAUSE_STATUS'.

Table S43.  Basic characteristics of clinical feature: 'MENOPAUSE_STATUS'

MENOPAUSE_STATUS Labels N
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL) 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD) 15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY) 68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT) 105
     
  Significant markers N = 9
List of 9 genes differentially expressed by 'MENOPAUSE_STATUS'

Table S44.  Get Full Table List of 9 genes differentially expressed by 'MENOPAUSE_STATUS'

ANOVA_P Q
C21ORF34 4.143e-07 0.00827
MIR99A 4.143e-07 0.00827
MIRLET7C 4.143e-07 0.00827
RARB 9.742e-07 0.0195
SSBP3 1.361e-06 0.0272
CD9 4.832e-06 0.0965
EML4 7.563e-06 0.151
KCNC4 9.986e-06 0.199
FBXW11 1.206e-05 0.241
Clinical variable #33: 'LYMPHOVASCULAR_INVOLVEMENT'

3 genes related to 'LYMPHOVASCULAR_INVOLVEMENT'.

Table S45.  Basic characteristics of clinical feature: 'LYMPHOVASCULAR_INVOLVEMENT'

LYMPHOVASCULAR_INVOLVEMENT Labels N
  ABSENT 68
  PRESENT 74
     
  Significant markers N = 3
  Higher in PRESENT 3
  Higher in ABSENT 0
List of 3 genes differentially expressed by 'LYMPHOVASCULAR_INVOLVEMENT'

Table S46.  Get Full Table List of 3 genes differentially expressed by 'LYMPHOVASCULAR_INVOLVEMENT'

W(pos if higher in 'PRESENT') wilcoxontestP Q AUC
ZNF445 c("3622", "6.346e-06") c("3622", "6.346e-06") 0.127 0.7198
MKRN2 c("3604", "8.954e-06") c("3604", "8.954e-06") 0.179 0.7162
TMEM87B c("1425", "1.306e-05") c("1425", "1.306e-05") 0.261 0.7129
Clinical variable #34: 'LYMPH_NODES_EXAMINED_HE_COUNT'

2 genes related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

Table S47.  Basic characteristics of clinical feature: 'LYMPH_NODES_EXAMINED_HE_COUNT'

LYMPH_NODES_EXAMINED_HE_COUNT Mean (SD) 1.04 (2.4)
  Significant markers N = 2
  pos. correlated 2
  neg. correlated 0
List of 2 genes differentially expressed by 'LYMPH_NODES_EXAMINED_HE_COUNT'

Table S48.  Get Full Table List of 2 genes significantly correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT' by Spearman correlation test

SpearmanCorr corrP Q
RCAN1 0.4235 1.515e-07 0.00303
NUAK1 0.3779 3.547e-06 0.0708
Clinical variable #35: 'LYMPH_NODES_EXAMINED'

No gene related to 'LYMPH_NODES_EXAMINED'.

Table S49.  Basic characteristics of clinical feature: 'LYMPH_NODES_EXAMINED'

LYMPH_NODES_EXAMINED Mean (SD) 21.66 (12)
  Significant markers N = 0
Clinical variable #36: 'KERATINIZATION_SQUAMOUS_CELL'

No gene related to 'KERATINIZATION_SQUAMOUS_CELL'.

Table S50.  Basic characteristics of clinical feature: 'KERATINIZATION_SQUAMOUS_CELL'

KERATINIZATION_SQUAMOUS_CELL Labels N
  KERATINIZING SQUAMOUS CELL CARCINOMA 49
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA 96
     
  Significant markers N = 0
Clinical variable #37: 'INITIAL_PATHOLOGIC_DX_YEAR'

221 genes related to 'INITIAL_PATHOLOGIC_DX_YEAR'.

Table S51.  Basic characteristics of clinical feature: 'INITIAL_PATHOLOGIC_DX_YEAR'

INITIAL_PATHOLOGIC_DX_YEAR Mean (SD) 2007.68 (5)
  Significant markers N = 221
  pos. correlated 5
  neg. correlated 216
List of top 10 genes differentially expressed by 'INITIAL_PATHOLOGIC_DX_YEAR'

Table S52.  Get Full Table List of top 10 genes significantly correlated to 'INITIAL_PATHOLOGIC_DX_YEAR' by Spearman correlation test

SpearmanCorr corrP Q
EBNA1BP2__1 -0.4177 1.365e-11 2.73e-07
WDR65__1 -0.4177 1.365e-11 2.73e-07
MMD -0.413 2.41e-11 4.81e-07
C21ORF57 -0.3897 3.648e-10 7.29e-06
HIST2H2AB -0.3843 6.671e-10 1.33e-05
OBFC2B -0.3817 8.912e-10 1.78e-05
NUP153 -0.3782 1.304e-09 2.6e-05
ST6GALNAC6 -0.3698 3.171e-09 6.33e-05
C9ORF82 -0.368 3.835e-09 7.66e-05
ZNF320 -0.3675 4.052e-09 8.09e-05
Clinical variable #38: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

No gene related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.

Table S53.  Basic characteristics of clinical feature: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

HISTORY_HORMONAL_CONTRACEPTIVES_USE Labels N
  CURRENT USER 10
  FORMER USER 47
  NEVER USED 58
     
  Significant markers N = 0
Clinical variable #39: 'HEIGHT_CM_AT_DIAGNOSIS'

No gene related to 'HEIGHT_CM_AT_DIAGNOSIS'.

Table S54.  Basic characteristics of clinical feature: 'HEIGHT_CM_AT_DIAGNOSIS'

HEIGHT_CM_AT_DIAGNOSIS Mean (SD) 161.69 (7)
  Significant markers N = 0
Clinical variable #40: 'CORPUS_INVOLVEMENT'

No gene related to 'CORPUS_INVOLVEMENT'.

Table S55.  Basic characteristics of clinical feature: 'CORPUS_INVOLVEMENT'

CORPUS_INVOLVEMENT Labels N
  ABSENT 95
  PRESENT 17
     
  Significant markers N = 0
Clinical variable #41: 'CHEMO_CONCURRENT_TYPE'

No gene related to 'CHEMO_CONCURRENT_TYPE'.

Table S56.  Basic characteristics of clinical feature: 'CHEMO_CONCURRENT_TYPE'

CHEMO_CONCURRENT_TYPE Labels N
  CARBOPLATIN 3
  CISPLATIN 18
  OTHER 1
     
  Significant markers N = 0
Clinical variable #42: 'CERVIX_SUV_RESULTS'

2 genes related to 'CERVIX_SUV_RESULTS'.

Table S57.  Basic characteristics of clinical feature: 'CERVIX_SUV_RESULTS'

CERVIX_SUV_RESULTS Mean (SD) 12.43 (5.5)
  Significant markers N = 2
  pos. correlated 0
  neg. correlated 2
List of 2 genes differentially expressed by 'CERVIX_SUV_RESULTS'

Table S58.  Get Full Table List of 2 genes significantly correlated to 'CERVIX_SUV_RESULTS' by Spearman correlation test

SpearmanCorr corrP Q
C11ORF87 -0.8901 0 0
MRPL28 -0.8846 0 0
Clinical variable #43: 'AJCC_TUMOR_PATHOLOGIC_PT'

No gene related to 'AJCC_TUMOR_PATHOLOGIC_PT'.

Table S59.  Basic characteristics of clinical feature: 'AJCC_TUMOR_PATHOLOGIC_PT'

AJCC_TUMOR_PATHOLOGIC_PT Labels N
  T1A 1
  T1A1 1
  T1B 32
  T1B1 66
  T1B2 25
  T2 4
  T2A 8
  T2A1 7
  T2A2 10
  T2B 19
  T3 1
  T3B 7
  T4 4
  TIS 1
  TX 15
     
  Significant markers N = 0
Clinical variable #44: 'AGE_AT_DIAGNOSIS'

30 genes related to 'AGE_AT_DIAGNOSIS'.

Table S60.  Basic characteristics of clinical feature: 'AGE_AT_DIAGNOSIS'

AGE_AT_DIAGNOSIS Mean (SD) 47.51 (14)
  Significant markers N = 30
  pos. correlated 9
  neg. correlated 21
List of top 10 genes differentially expressed by 'AGE_AT_DIAGNOSIS'

Table S61.  Get Full Table List of top 10 genes significantly correlated to 'AGE_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
RARB -0.355 1.253e-08 0.00025
OAZ2 -0.3379 6.647e-08 0.00133
CHRNB1 0.3225 2.748e-07 0.00549
CDIPT -0.312 6.956e-07 0.0139
LOC440356 -0.312 6.956e-07 0.0139
SP4 -0.3024 1.57e-06 0.0313
EYA4 0.3019 1.638e-06 0.0327
HMGCS1 -0.3007 1.809e-06 0.0361
CD9 -0.2996 1.982e-06 0.0396
ZBTB5 -0.2884 4.883e-06 0.0975
Clinical variable #45: 'STAGE_EVENT.CLINICAL_STAGE'

No gene related to 'STAGE_EVENT.CLINICAL_STAGE'.

Table S62.  Basic characteristics of clinical feature: 'STAGE_EVENT.CLINICAL_STAGE'

STAGE_EVENT.CLINICAL_STAGE Labels N
  STAGE I 4
  STAGE IA 2
  STAGE IA1 1
  STAGE IA2 1
  STAGE IB 35
  STAGE IB1 68
  STAGE IB2 34
  STAGE II 4
  STAGE IIA 7
  STAGE IIA1 5
  STAGE IIA2 7
  STAGE IIB 23
  STAGE III 1
  STAGE IIIB 33
  STAGE IVA 5
  STAGE IVB 7
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 243

  • Number of genes = 19971

  • Number of clinical features = 45

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

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] 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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