Correlation between gene methylation status and clinical features
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1FB51PT
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/C1FB51PT
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 20048 genes and 43 clinical features across 200 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 15 clinical features related to at least one genes.

  • 84 genes correlated to 'Time to Death'.

    • SLC25A16 ,  NDUFC1 ,  ARMC8 ,  BTAF1 ,  MRPL50 ,  ...

  • 29 genes correlated to 'AGE'.

    • RARB ,  CHRNB1 ,  OAZ2 ,  EIF4G2 ,  SNORD97 ,  ...

  • 1932 genes correlated to 'HISTOLOGICAL.TYPE'.

    • ATP10D ,  GPR87 ,  MED12L__5 ,  DNALI1 ,  DST ,  ...

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

    • CEP97 ,  NR4A1 ,  C22ORF26__1 ,  LOC150381__1 ,  C9ORF82 ,  ...

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

    • RCAN1 ,  PPARGC1A

  • 1 gene correlated to 'WEIGHT_KG_AT_DIAGNOSIS'.

    • RUVBL1

  • 9 genes correlated to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.

    • HSBP1 ,  CXXC1 ,  ZNF346 ,  KLHL32 ,  AFG3L1 ,  ...

  • 1 gene correlated to 'PATIENT.AGEBEGANSMOKINGINYEARS'.

    • IFT57

  • 67 genes correlated to 'RADIATION_THERAPY_TYPE'.

    • C22ORF26__1 ,  LOC150381__1 ,  C1ORF204__1 ,  VSIG8__1 ,  PRPF6 ,  ...

  • 1 gene correlated to 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.

    • FGB

  • 5 genes correlated to 'MENOPAUSE_STATUS'.

    • RARB ,  C21ORF34 ,  MIR99A ,  MIRLET7C ,  PHGDH

  • 2 genes correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

    • RCAN1 ,  PPARGC1A

  • 126 genes correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.

    • GPR113 ,  SELI ,  EBNA1BP2__1 ,  WDR65__1 ,  C9ORF82 ,  ...

  • 14 genes correlated to 'CERVIX_SUV_RESULTS'.

    • B3GNT3 ,  BTBD9 ,  C2CD4B ,  CCNE2 ,  FKRP ,  ...

  • 32 genes correlated to 'AGE_AT_DIAGNOSIS'.

    • RARB ,  OAZ2 ,  CHRNB1 ,  MLF1IP ,  EIF4G2 ,  ...

  • No genes correlated to 'PATHOLOGY.T.STAGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'NUMBERPACKYEARSSMOKED', 'RACE', 'ETHNICITY', 'TUMOR_STATUS', 'NEOPLASMHISTOLOGICGRADE', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_PACK_YEARS_SMOKED', 'TOBACCO_SMOKING_HISTORY', 'RADIATION_ADJUVANT_UNITS', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PREGNANCIES_COUNT_LIVE_BIRTH', 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT', 'PREGNANCIES_COUNT_ECTOPIC', 'LYMPH_NODE_LOCATION', 'LOCATION_OF_POSITIVE_MARGINS', 'LYMPHOVASCULAR_INVOLVEMENT', 'LYMPH_NODES_EXAMINED', 'KERATINIZATION_SQUAMOUS_CELL', 'HYSTERECTOMY_TYPE', 'HISTORY_HORMONAL_CONTRACEPTIVES_USE', 'HEIGHT_CM_AT_DIAGNOSIS', 'CORPUS_INVOLVEMENT', 'CHEMO_CONCURRENT_TYPE', and 'AJCC_TUMOR_PATHOLOGIC_PT'.

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=84 shorter survival N=83 longer survival N=1
AGE Spearman correlation test N=29 older N=6 younger N=23
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=1932        
RADIATIONS RADIATION REGIMENINDICATION Wilcoxon test N=216 yes N=216 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=0        
ETHNICITY Wilcoxon test   N=0        
WEIGHT_KG_AT_DIAGNOSIS Spearman correlation test N=1 higher weight_kg_at_diagnosis N=1 lower weight_kg_at_diagnosis N=0
TUMOR_STATUS Wilcoxon test   N=0        
TUMOR_SAMPLE_PROCUREMENT_COUNTRY Kruskal-Wallis test N=9        
NEOPLASMHISTOLOGICGRADE Kruskal-Wallis test   N=0        
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=1 higher patient.agebegansmokinginyears N=0 lower patient.agebegansmokinginyears N=1
RADIATION_THERAPY_TYPE Kruskal-Wallis test N=67        
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=1 higher patient.patientpregnancyspontaneousabortioncount N=1 lower patient.patientpregnancyspontaneousabortioncount N=0
PREGNANCIES_COUNT_LIVE_BIRTH Spearman correlation test   N=0        
PATIENT PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT Spearman correlation test   N=0        
PREGNANCIES_COUNT_ECTOPIC Spearman correlation test   N=0        
LYMPH_NODE_LOCATION Kruskal-Wallis test   N=0        
LOCATION_OF_POSITIVE_MARGINS Kruskal-Wallis test   N=0        
MENOPAUSE_STATUS Kruskal-Wallis test N=5        
LYMPHOVASCULAR_INVOLVEMENT Wilcoxon test   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=126 higher initial_pathologic_dx_year N=3 lower initial_pathologic_dx_year N=123
HYSTERECTOMY_TYPE Kruskal-Wallis test   N=0        
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 Wilcoxon test   N=0        
CERVIX_SUV_RESULTS Spearman correlation test N=14 higher cervix_suv_results N=5 lower cervix_suv_results N=9
AJCC_TUMOR_PATHOLOGIC_PT Kruskal-Wallis test   N=0        
AGE_AT_DIAGNOSIS Spearman correlation test N=32 higher age_at_diagnosis N=7 lower age_at_diagnosis N=25
Clinical variable #1: 'Time to Death'

84 genes related to 'Time to Death'.

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

Time to Death Duration (Months) 0-182.9 (median=13.9)
  censored N = 155
  death N = 38
     
  Significant markers N = 84
  associated with shorter survival 83
  associated with longer survival 1
List of top 10 genes differentially expressed by 'Time to Death'

Table S2.  Get Full Table List of top 10 genes significantly associated with 'Time to Death' by Cox regression test

HazardRatio Wald_P Q C_index
SLC25A16 4.1e+34 3.915e-08 0.00078 0.724
NDUFC1 1.9e+39 1.085e-07 0.0022 0.687
ARMC8 190000000000001 2.662e-07 0.0053 0.689
BTAF1 7.1e+17 3.284e-07 0.0066 0.669
MRPL50 9.1e+19 7.162e-07 0.014 0.694
ZNF189 9.1e+19 7.162e-07 0.014 0.694
SRPK1 790000000000001 7.602e-07 0.015 0.656
RPA3 2.1e+32 1.149e-06 0.023 0.618
RP9 1.2e+31 1.261e-06 0.025 0.641
CCDC7 7.5e+18 1.978e-06 0.04 0.684
Clinical variable #2: 'AGE'

29 genes related to 'AGE'.

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

AGE Mean (SD) 47.48 (13)
  Significant markers N = 29
  pos. correlated 6
  neg. correlated 23
List of top 10 genes differentially expressed by 'AGE'

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

SpearmanCorr corrP Q
RARB -0.4186 7.591e-10 1.52e-05
CHRNB1 0.3574 2.187e-07 0.00438
OAZ2 -0.354 2.896e-07 0.00581
EIF4G2 -0.345 6.008e-07 0.012
SNORD97 -0.345 6.008e-07 0.012
MLF1IP -0.3441 6.931e-07 0.0139
ZBTB5 -0.327 2.431e-06 0.0487
SP4 -0.3223 3.441e-06 0.069
PHGDH -0.317 5.082e-06 0.102
CDIPT -0.3166 5.223e-06 0.105
Clinical variable #3: 'PATHOLOGY.T.STAGE'

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

Table S5.  Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE Mean (SD) 1.32 (0.57)
  N
  1 108
  2 39
  3 2
  4 2
     
  Significant markers N = 0
Clinical variable #4: 'PATHOLOGY.N.STAGE'

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

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

PATHOLOGY.N.STAGE Labels N
  class0 100
  class1 44
     
  Significant markers N = 0
Clinical variable #5: 'PATHOLOGY.M.STAGE'

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

Table S7.  Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE Labels N
  M0 83
  M1 4
  MX 70
     
  Significant markers N = 0
Clinical variable #6: 'HISTOLOGICAL.TYPE'

1932 genes related to 'HISTOLOGICAL.TYPE'.

Table S8.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  ADENOSQUAMOUS 2
  CERVICAL SQUAMOUS CELL CARCINOMA 168
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA 20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE 4
     
  Significant markers N = 1932
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S9.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
ATP10D 7.169e-15 1.44e-10
GPR87 2.932e-14 5.88e-10
MED12L__5 2.932e-14 5.88e-10
DNALI1 3.786e-14 7.59e-10
DST 3.853e-14 7.72e-10
TMEM117 4.014e-14 8.05e-10
DAB2IP 4.27e-14 8.56e-10
RILPL1 4.438e-14 8.89e-10
OGDH 5.315e-14 1.07e-09
RGS12 6.571e-14 1.32e-09
Clinical variable #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

Table S10.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 32
  YES 168
     
  Significant markers N = 216
  Higher in YES 216
  Higher in NO 0
List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S11.  Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

W(pos if higher in 'YES') wilcoxontestP Q AUC
CEP97 855 1.017e-09 2.04e-05 0.841
NR4A1 887 1.972e-09 3.95e-05 0.835
C22ORF26__1 894 2.276e-09 4.56e-05 0.8337
LOC150381__1 894 2.276e-09 4.56e-05 0.8337
C9ORF82 898 2.47e-09 4.95e-05 0.833
CDKN2AIPNL 920 3.86e-09 7.74e-05 0.8289
PMPCA 947 6.627e-09 0.000133 0.8238
CEPT1 973 1.107e-08 0.000222 0.819
DRAM2 973 1.107e-08 0.000222 0.819
CAPS2 977 1.197e-08 0.00024 0.8183
Clinical variable #8: 'NUMBERPACKYEARSSMOKED'

No gene related to 'NUMBERPACKYEARSSMOKED'.

Table S12.  Basic characteristics of clinical feature: 'NUMBERPACKYEARSSMOKED'

NUMBERPACKYEARSSMOKED Mean (SD) 19.43 (14)
  Significant markers N = 0
Clinical variable #9: 'NUMBER.OF.LYMPH.NODES'

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

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

NUMBER.OF.LYMPH.NODES Mean (SD) 1.07 (2.6)
  Significant markers N = 2
  pos. correlated 2
  neg. correlated 0
List of 2 genes differentially expressed by 'NUMBER.OF.LYMPH.NODES'

Table S14.  Get Full Table List of 2 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
RCAN1 0.3949 6.177e-06 0.124
PPARGC1A 0.3897 8.401e-06 0.168
Clinical variable #10: 'RACE'

No gene related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 7
  ASIAN 16
  BLACK OR AFRICAN AMERICAN 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 1
  WHITE 148
     
  Significant markers N = 0
Clinical variable #11: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 13
  NOT HISPANIC OR LATINO 144
     
  Significant markers N = 0
Clinical variable #12: 'WEIGHT_KG_AT_DIAGNOSIS'

One gene related to 'WEIGHT_KG_AT_DIAGNOSIS'.

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

WEIGHT_KG_AT_DIAGNOSIS Mean (SD) 75.21 (21)
  Significant markers N = 1
  pos. correlated 1
  neg. correlated 0
List of one gene differentially expressed by 'WEIGHT_KG_AT_DIAGNOSIS'

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

SpearmanCorr corrP Q
RUVBL1 0.3631 4.724e-07 0.00947
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 51
  WITH TUMOR 22
     
  Significant markers N = 0
Clinical variable #14: 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

9 genes related to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.

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

TUMOR_SAMPLE_PROCUREMENT_COUNTRY Labels N
  NIGERIA 1
  RUSSIA 11
  UKRAINE 7
  UNITED STATES 169
  VIETNAM 12
     
  Significant markers N = 9
List of 9 genes differentially expressed by 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

Table S21.  Get Full Table List of 9 genes differentially expressed by 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

ANOVA_P Q
HSBP1 1.349e-07 0.0027
CXXC1 8.992e-07 0.018
ZNF346 4.126e-06 0.0827
KLHL32 5.276e-06 0.106
AFG3L1 6.326e-06 0.127
CENPBD1 6.326e-06 0.127
DICER1__1 6.587e-06 0.132
FLJ45244 6.587e-06 0.132
GJC3 9.507e-06 0.191
Clinical variable #15: 'NEOPLASMHISTOLOGICGRADE'

No gene related to 'NEOPLASMHISTOLOGICGRADE'.

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

NEOPLASMHISTOLOGICGRADE Labels N
  G1 14
  G2 94
  G3 83
  G4 1
  GX 5
     
  Significant markers N = 0
Clinical variable #16: 'TOBACCO_SMOKING_YEAR_STOPPED'

No gene related to 'TOBACCO_SMOKING_YEAR_STOPPED'.

Table S23.  Basic characteristics of clinical feature: 'TOBACCO_SMOKING_YEAR_STOPPED'

TOBACCO_SMOKING_YEAR_STOPPED Mean (SD) 1998.37 (12)
  Significant markers N = 0
Clinical variable #17: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'

No gene related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.

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

TOBACCO_SMOKING_PACK_YEARS_SMOKED Mean (SD) 19.43 (14)
  Significant markers N = 0
Clinical variable #18: 'TOBACCO_SMOKING_HISTORY'

No gene related to 'TOBACCO_SMOKING_HISTORY'.

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

TOBACCO_SMOKING_HISTORY Labels N
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS 25
  CURRENT REFORMED SMOKER FOR > 15 YEARS 8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED 3
  CURRENT SMOKER 43
  LIFELONG NON-SMOKER 89
     
  Significant markers N = 0
Clinical variable #19: 'PATIENT.AGEBEGANSMOKINGINYEARS'

One gene related to 'PATIENT.AGEBEGANSMOKINGINYEARS'.

Table S26.  Basic characteristics of clinical feature: 'PATIENT.AGEBEGANSMOKINGINYEARS'

PATIENT.AGEBEGANSMOKINGINYEARS Mean (SD) 20.46 (6.2)
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one gene differentially expressed by 'PATIENT.AGEBEGANSMOKINGINYEARS'

Table S27.  Get Full Table List of one gene significantly correlated to 'PATIENT.AGEBEGANSMOKINGINYEARS' by Spearman correlation test

SpearmanCorr corrP Q
IFT57 -0.5681 7.424e-06 0.149
Clinical variable #20: 'RADIATION_THERAPY_TYPE'

67 genes related to 'RADIATION_THERAPY_TYPE'.

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

RADIATION_THERAPY_TYPE Labels N
  COMBINATION 18
  EXTERNAL 44
  EXTERNAL BEAM 14
  IMPLANTS 1
  INTERNAL 8
     
  Significant markers N = 67
List of top 10 genes differentially expressed by 'RADIATION_THERAPY_TYPE'

Table S29.  Get Full Table List of top 10 genes differentially expressed by 'RADIATION_THERAPY_TYPE'

ANOVA_P Q
C22ORF26__1 5.243e-09 0.000105
LOC150381__1 5.243e-09 0.000105
C1ORF204__1 1.938e-08 0.000388
VSIG8__1 1.938e-08 0.000388
PRPF6 4.794e-08 0.000961
TMEM67 5.717e-08 0.00115
HIST2H2AB 8.823e-08 0.00177
C9ORF82 1.699e-07 0.00341
CDKN2AIPNL 2.856e-07 0.00572
ST6GALNAC6 5.073e-07 0.0102
Clinical variable #21: 'RADIATION_ADJUVANT_UNITS'

No gene related to 'RADIATION_ADJUVANT_UNITS'.

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

RADIATION_ADJUVANT_UNITS Labels N
  CGY 16
  GY 4
     
  Significant markers N = 0
Clinical variable #22: 'PREGNANCIES_COUNT_TOTAL'

No gene related to 'PREGNANCIES_COUNT_TOTAL'.

Table S31.  Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_TOTAL'

PREGNANCIES_COUNT_TOTAL Mean (SD) 3.49 (2.4)
  Significant markers N = 0
Clinical variable #23: 'PREGNANCIES_COUNT_STILLBIRTH'

No gene related to 'PREGNANCIES_COUNT_STILLBIRTH'.

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

PREGNANCIES_COUNT_STILLBIRTH Mean (SD) 0.08 (0.37)
  Value N
  0 94
  1 5
  3 1
     
  Significant markers N = 0
Clinical variable #24: 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

One gene related to 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.

Table S33.  Basic characteristics of clinical feature: 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT Mean (SD) 0.35 (0.59)
  Value N
  0 81
  1 30
  2 4
  3 1
     
  Significant markers N = 1
  pos. correlated 1
  neg. correlated 0
List of one gene differentially expressed by 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

Table S34.  Get Full Table List of one gene significantly correlated to 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT' by Spearman correlation test

SpearmanCorr corrP Q
FGB 0.4497 4.105e-07 0.00823
Clinical variable #25: 'PREGNANCIES_COUNT_LIVE_BIRTH'

No gene related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

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

PREGNANCIES_COUNT_LIVE_BIRTH Mean (SD) 2.47 (1.8)
  Significant markers N = 0
Clinical variable #26: 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

No gene related to 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.

Table S36.  Basic characteristics of clinical feature: 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT Mean (SD) 0.91 (1.9)
  Significant markers N = 0
Clinical variable #27: 'PREGNANCIES_COUNT_ECTOPIC'

No gene related to 'PREGNANCIES_COUNT_ECTOPIC'.

Table S37.  Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_ECTOPIC'

PREGNANCIES_COUNT_ECTOPIC Mean (SD) 0.1 (0.33)
  Value N
  0 92
  1 8
  2 1
     
  Significant markers N = 0
Clinical variable #28: 'LYMPH_NODE_LOCATION'

No gene related to 'LYMPH_NODE_LOCATION'.

Table S38.  Basic characteristics of clinical feature: 'LYMPH_NODE_LOCATION'

LYMPH_NODE_LOCATION Labels N
  2003 1
  2010 1
  COMMON ILIAC 1
  PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR) 41
     
  Significant markers N = 0
Clinical variable #29: 'LOCATION_OF_POSITIVE_MARGINS'

No gene related to 'LOCATION_OF_POSITIVE_MARGINS'.

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

LOCATION_OF_POSITIVE_MARGINS Labels N
  MACROSCOPIC PARAMETRIAL INVOLVEMENT 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT 7
  OTHER LOCATION, SPECIFY 13
  POSITIVE BLADDER MARGIN 1
  POSITIVE VAGINAL MARGIN 6
     
  Significant markers N = 0
Clinical variable #30: 'MENOPAUSE_STATUS'

5 genes related to 'MENOPAUSE_STATUS'.

Table S40.  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) 10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY) 58
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT) 85
     
  Significant markers N = 5
List of 5 genes differentially expressed by 'MENOPAUSE_STATUS'

Table S41.  Get Full Table List of 5 genes differentially expressed by 'MENOPAUSE_STATUS'

ANOVA_P Q
RARB 9.798e-08 0.00196
C21ORF34 3.329e-07 0.00667
MIR99A 3.329e-07 0.00667
MIRLET7C 3.329e-07 0.00667
PHGDH 5.602e-06 0.112
Clinical variable #31: 'LYMPHOVASCULAR_INVOLVEMENT'

No gene related to 'LYMPHOVASCULAR_INVOLVEMENT'.

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

LYMPHOVASCULAR_INVOLVEMENT Labels N
  ABSENT 56
  PRESENT 66
     
  Significant markers N = 0
Clinical variable #32: 'LYMPH_NODES_EXAMINED_HE_COUNT'

2 genes related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

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

LYMPH_NODES_EXAMINED_HE_COUNT Mean (SD) 1.07 (2.6)
  Significant markers N = 2
  pos. correlated 2
  neg. correlated 0
List of 2 genes differentially expressed by 'LYMPH_NODES_EXAMINED_HE_COUNT'

Table S44.  Get Full Table List of 2 genes significantly correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT' by Spearman correlation test

SpearmanCorr corrP Q
RCAN1 0.3949 6.177e-06 0.124
PPARGC1A 0.3897 8.401e-06 0.168
Clinical variable #33: 'LYMPH_NODES_EXAMINED'

No gene related to 'LYMPH_NODES_EXAMINED'.

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

LYMPH_NODES_EXAMINED Mean (SD) 22.39 (13)
  Significant markers N = 0
Clinical variable #34: 'KERATINIZATION_SQUAMOUS_CELL'

No gene related to 'KERATINIZATION_SQUAMOUS_CELL'.

Table S46.  Basic characteristics of clinical feature: 'KERATINIZATION_SQUAMOUS_CELL'

KERATINIZATION_SQUAMOUS_CELL Labels N
  KERATINIZING SQUAMOUS CELL CARCINOMA 43
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA 88
     
  Significant markers N = 0
Clinical variable #35: 'INITIAL_PATHOLOGIC_DX_YEAR'

126 genes related to 'INITIAL_PATHOLOGIC_DX_YEAR'.

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

INITIAL_PATHOLOGIC_DX_YEAR Mean (SD) 2007.28 (5.2)
  Significant markers N = 126
  pos. correlated 3
  neg. correlated 123
List of top 10 genes differentially expressed by 'INITIAL_PATHOLOGIC_DX_YEAR'

Table S48.  Get Full Table List of top 10 genes significantly correlated to 'INITIAL_PATHOLOGIC_DX_YEAR' by Spearman correlation test

SpearmanCorr corrP Q
GPR113 -0.4716 1.816e-12 3.64e-08
SELI -0.4716 1.816e-12 3.64e-08
EBNA1BP2__1 -0.4424 5.449e-11 1.09e-06
WDR65__1 -0.4424 5.449e-11 1.09e-06
C9ORF82 -0.4306 1.955e-10 3.92e-06
MMD -0.4171 8.078e-10 1.62e-05
HIST2H2AB -0.412 1.347e-09 2.7e-05
ERAL1 -0.3948 7.261e-09 0.000146
ZNF320 -0.3916 9.836e-09 0.000197
DCDC1 -0.3844 1.921e-08 0.000385
Clinical variable #36: 'HYSTERECTOMY_TYPE'

No gene related to 'HYSTERECTOMY_TYPE'.

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

HYSTERECTOMY_TYPE Labels N
  OTHER 3
  RADICAL HYSTERECTOMY 129
  SIMPLE HYSTERECTOMY 5
     
  Significant markers N = 0
Clinical variable #37: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

No gene related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.

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

HISTORY_HORMONAL_CONTRACEPTIVES_USE Labels N
  CURRENT USER 8
  FORMER USER 40
  NEVER USED 47
     
  Significant markers N = 0
Clinical variable #38: 'HEIGHT_CM_AT_DIAGNOSIS'

No gene related to 'HEIGHT_CM_AT_DIAGNOSIS'.

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

HEIGHT_CM_AT_DIAGNOSIS Mean (SD) 162.09 (7.2)
  Significant markers N = 0
Clinical variable #39: 'CORPUS_INVOLVEMENT'

No gene related to 'CORPUS_INVOLVEMENT'.

Table S52.  Basic characteristics of clinical feature: 'CORPUS_INVOLVEMENT'

CORPUS_INVOLVEMENT Labels N
  ABSENT 81
  PRESENT 15
     
  Significant markers N = 0
Clinical variable #40: 'CHEMO_CONCURRENT_TYPE'

No gene related to 'CHEMO_CONCURRENT_TYPE'.

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

CHEMO_CONCURRENT_TYPE Labels N
  CARBOPLATIN 3
  CISPLATIN 17
     
  Significant markers N = 0
Clinical variable #41: 'CERVIX_SUV_RESULTS'

14 genes related to 'CERVIX_SUV_RESULTS'.

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

CERVIX_SUV_RESULTS Mean (SD) 12.84 (6.1)
  Significant markers N = 14
  pos. correlated 5
  neg. correlated 9
List of top 10 genes differentially expressed by 'CERVIX_SUV_RESULTS'

Table S55.  Get Full Table List of top 10 genes significantly correlated to 'CERVIX_SUV_RESULTS' by Spearman correlation test

SpearmanCorr corrP Q
B3GNT3 -0.9515 0 0
BTBD9 0.9394 0 0
C2CD4B 0.9394 0 0
CCNE2 0.9394 0 0
FKRP -0.9394 0 0
HEY1 0.9394 0 0
MBOAT7__1 -0.9515 0 0
NACC1__1 -0.9879 0 0
PRSS16 -0.9394 0 0
PTS -0.9515 0 0
Clinical variable #42: 'AJCC_TUMOR_PATHOLOGIC_PT'

No gene related to 'AJCC_TUMOR_PATHOLOGIC_PT'.

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

AJCC_TUMOR_PATHOLOGIC_PT Labels N
  T1A 2
  T1A1 1
  T1B 26
  T1B1 55
  T1B2 24
  T2 3
  T2A 6
  T2A1 7
  T2A2 9
  T2B 14
  T3B 2
  T4 2
  TIS 1
  TX 8
     
  Significant markers N = 0
Clinical variable #43: 'AGE_AT_DIAGNOSIS'

32 genes related to 'AGE_AT_DIAGNOSIS'.

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

AGE_AT_DIAGNOSIS Mean (SD) 47.55 (13)
  Significant markers N = 32
  pos. correlated 7
  neg. correlated 25
List of top 10 genes differentially expressed by 'AGE_AT_DIAGNOSIS'

Table S58.  Get Full Table List of top 10 genes significantly correlated to 'AGE_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
RARB -0.4091 1.809e-09 3.63e-05
OAZ2 -0.3578 1.98e-07 0.00397
CHRNB1 0.3452 5.543e-07 0.0111
MLF1IP -0.346 5.578e-07 0.0112
EIF4G2 -0.342 7.179e-07 0.0144
SNORD97 -0.342 7.179e-07 0.0144
ZBTB5 -0.3275 2.201e-06 0.0441
CDIPT -0.3224 3.218e-06 0.0645
LOC440356 -0.3224 3.218e-06 0.0645
SP4 -0.3222 3.275e-06 0.0656
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 = 200

  • Number of genes = 20048

  • Number of clinical features = 43

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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