Correlation between gene methylation status and clinical features
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1736Q24
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene methylation status and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1736Q24
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 19994 genes and 39 clinical features across 307 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 17 clinical features related to at least one genes.

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • C21ORF34 ,  MIR99A ,  MIRLET7C ,  SP4 ,  GLDC ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • CLCA3P ,  NUP35 ,  PMCH ,  MPP7 ,  DKFZP586I1420 ,  ...

  • 30 genes correlated to 'RADIATION_THERAPY'.

    • MGST2 ,  PHF17 ,  HLA-DRB1 ,  PDCL ,  CNOT3 ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • ATP10D ,  C10ORF108 ,  DIP2C ,  TMEM117 ,  GPR87 ,  ...

  • 30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

    • RCAN1 ,  NUAK1 ,  BCL9 ,  ARIH2__1 ,  C3ORF71__1 ,  ...

  • 30 genes correlated to 'RACE'.

    • SNX16 ,  PDXDC1 ,  IFNGR2 ,  TLE1 ,  NDUFS5 ,  ...

  • 30 genes correlated to 'TUMOR_STATUS'.

    • PATL2 ,  CCR5 ,  FAM35B2 ,  CHRM3 ,  MPDU1 ,  ...

  • 30 genes correlated to 'NEOPLASM_HISTOLOGIC_GRADE'.

    • GMNN ,  MTF2 ,  MRPS9 ,  BRIX1__1 ,  RAD1__1 ,  ...

  • 30 genes correlated to 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT'.

    • GPRIN1 ,  TAF3 ,  POLR2D ,  C8ORF77 ,  ZNF252 ,  ...

  • 30 genes correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

    • POLE ,  PXMP2 ,  ZNF488 ,  PALM3 ,  PGF ,  ...

  • 30 genes correlated to 'MENOPAUSE_STATUS'.

    • C21ORF34 ,  MIR99A ,  MIRLET7C ,  RARB ,  FBXW11 ,  ...

  • 30 genes correlated to 'LYMPHOVASCULAR_INVOLVEMENT'.

    • MKRN2 ,  ZNF197 ,  HYAL3__1 ,  NAT6__1 ,  TMEM87B ,  ...

  • 30 genes correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

    • RCAN1 ,  NUAK1 ,  BCL9 ,  ARIH2__1 ,  C3ORF71__1 ,  ...

  • 30 genes correlated to 'LYMPH_NODES_EXAMINED'.

    • LOC643837 ,  HDAC1 ,  NIPA1 ,  TTLL10 ,  CCDC134 ,  ...

  • 30 genes correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.

    • KLHL9 ,  MMD ,  RHOT2 ,  DCDC1 ,  DNAJC24 ,  ...

  • 30 genes correlated to 'AGE_AT_DIAGNOSIS'.

    • C21ORF34 ,  MIR99A ,  MIRLET7C ,  SP4 ,  GLDC ,  ...

  • 30 genes correlated to 'CLINICAL_STAGE'.

    • ARF4 ,  C3ORF48 ,  RAB5A ,  DPY30 ,  ZNF322B ,  ...

  • No genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'NUMBER_PACK_YEARS_SMOKED', 'ETHNICITY', 'WEIGHT_KG_AT_DIAGNOSIS', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_PACK_YEARS_SMOKED', 'TOBACCO_SMOKING_HISTORY', 'AGEBEGANSMOKINGINYEARS', 'RADIATION_THERAPY_STATUS', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT', 'PREGNANCIES_COUNT_ECTOPIC', 'POS_LYMPH_NODE_LOCATION', 'KERATINIZATION_SQUAMOUS_CELL', 'HISTORY_HORMONAL_CONTRACEPTIVES_USE', 'HEIGHT_CM_AT_DIAGNOSIS', 'CORPUS_INVOLVEMENT', 'CHEMO_CONCURRENT_TYPE', and 'CERVIX_SUV_RESULTS'.

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
DAYS_TO_DEATH_OR_LAST_FUP Cox regression test   N=0        
YEARS_TO_BIRTH Spearman correlation test N=30 older N=12 younger N=18
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=4 lower stage N=26
PATHOLOGY_N_STAGE Wilcoxon test   N=0        
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
RADIATION_THERAPY Wilcoxon test N=30 yes N=30 no N=0
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
NUMBER_PACK_YEARS_SMOKED Spearman correlation test   N=0        
NUMBER_OF_LYMPH_NODES Spearman correlation test N=30 higher number_of_lymph_nodes N=22 lower number_of_lymph_nodes N=8
RACE Kruskal-Wallis test N=30        
ETHNICITY Wilcoxon test   N=0        
WEIGHT_KG_AT_DIAGNOSIS Spearman correlation test   N=0        
TUMOR_STATUS Wilcoxon test N=30 with tumor N=30 tumor free N=0
NEOPLASM_HISTOLOGIC_GRADE Kruskal-Wallis test N=30        
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        
AGEBEGANSMOKINGINYEARS Spearman correlation test   N=0        
RADIATION_THERAPY_STATUS Wilcoxon test   N=0        
PREGNANCIES_COUNT_TOTAL Spearman correlation test   N=0        
PREGNANCIES_COUNT_STILLBIRTH Spearman correlation test   N=0        
PREGNANCY_SPONTANEOUS_ABORTION_COUNT Spearman correlation test N=30 higher pregnancy_spontaneous_abortion_count N=16 lower pregnancy_spontaneous_abortion_count N=14
PREGNANCIES_COUNT_LIVE_BIRTH Spearman correlation test N=30 higher pregnancies_count_live_birth N=12 lower pregnancies_count_live_birth N=18
PREGNANCY_THERAPEUTIC_ABORTION_COUNT 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=30        
LYMPHOVASCULAR_INVOLVEMENT Wilcoxon test N=30 present N=30 absent N=0
LYMPH_NODES_EXAMINED_HE_COUNT Spearman correlation test N=30 higher lymph_nodes_examined_he_count N=22 lower lymph_nodes_examined_he_count N=8
LYMPH_NODES_EXAMINED Spearman correlation test N=30 higher lymph_nodes_examined N=30 lower lymph_nodes_examined N=0
KERATINIZATION_SQUAMOUS_CELL Wilcoxon test   N=0        
INITIAL_PATHOLOGIC_DX_YEAR Spearman correlation test N=30 higher initial_pathologic_dx_year N=2 lower initial_pathologic_dx_year N=28
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=0        
AGE_AT_DIAGNOSIS Spearman correlation test N=30 higher age_at_diagnosis N=10 lower age_at_diagnosis N=20
CLINICAL_STAGE Kruskal-Wallis test N=30        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

No gene related to 'DAYS_TO_DEATH_OR_LAST_FUP'.

Table S1.  Basic characteristics of clinical feature: 'DAYS_TO_DEATH_OR_LAST_FUP'

DAYS_TO_DEATH_OR_LAST_FUP Duration (Months) 0-210.7 (median=23.8)
  censored N = 235
  death N = 71
     
  Significant markers N = 0
Clinical variable #2: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

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

YEARS_TO_BIRTH Mean (SD) 48.2 (14)
  Significant markers N = 30
  pos. correlated 12
  neg. correlated 18
List of top 10 genes differentially expressed by 'YEARS_TO_BIRTH'

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

SpearmanCorr corrP Q
C21ORF34 -0.3122 2.556e-08 0.00017
MIR99A -0.3122 2.556e-08 0.00017
MIRLET7C -0.3122 2.556e-08 0.00017
SP4 -0.3061 4.887e-08 0.000244
GLDC 0.3022 7.377e-08 0.000261
CHRNB1 0.3016 7.846e-08 0.000261
MDFI 0.2987 1.051e-07 3e-04
CCDC23 -0.2951 1.521e-07 0.000338
ERMAP -0.2951 1.521e-07 0.000338
GALNT2 0.2927 1.947e-07 0.000375
Clinical variable #3: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

Table S4.  Basic characteristics of clinical feature: 'PATHOLOGY_T_STAGE'

PATHOLOGY_T_STAGE Mean (SD) 1.59 (0.81)
  N
  T1 141
  T2 72
  T3 21
  T4 10
     
  Significant markers N = 30
  pos. correlated 4
  neg. correlated 26
List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S5.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
CLCA3P -0.3475 2.473e-08 0.000171
NUP35 0.3443 3.371e-08 0.000171
PMCH -0.3443 3.378e-08 0.000171
MPP7 -0.343 3.828e-08 0.000171
DKFZP586I1420 -0.3426 4.265e-08 0.000171
NCOA2 -0.3418 6.745e-08 0.000203
ATP6AP1L -0.3366 7.096e-08 0.000203
TANC2 -0.3322 1.075e-07 0.000269
TMEM86B -0.3293 1.405e-07 0.000305
MIR155 -0.3259 1.914e-07 0.000305
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
  N0 135
  N1 60
     
  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
  class0 116
  class1 10
     
  Significant markers N = 0
Clinical variable #6: 'RADIATION_THERAPY'

30 genes related to 'RADIATION_THERAPY'.

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

RADIATION_THERAPY Labels N
  NO 57
  YES 127
     
  Significant markers N = 30
  Higher in YES 30
  Higher in NO 0
List of top 10 genes differentially expressed by 'RADIATION_THERAPY'

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

W(pos if higher in 'YES') wilcoxontestP Q AUC
MGST2 5162 3.915e-06 0.0783 0.7131
PHF17 5062 1.585e-05 0.156 0.6993
HLA-DRB1 5008 3.255e-05 0.156 0.6918
PDCL 4990 4.114e-05 0.156 0.6893
CNOT3 2243 4.895e-05 0.156 0.6877
C20ORF11 2271 5.458e-05 0.156 0.6863
DIDO1__1 2271 5.458e-05 0.156 0.6863
LHX4 2317 9.723e-05 0.217 0.6799
CADPS2__2 2326 0.0001086 0.217 0.6787
RNF133 2326 0.0001086 0.217 0.6787
Clinical variable #7: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

Table S10.  Basic characteristics of clinical feature: 'HISTOLOGICAL_TYPE'

HISTOLOGICAL_TYPE Labels N
  ADENOSQUAMOUS 6
  CERVICAL SQUAMOUS CELL CARCINOMA 254
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA 21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE 17
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

Table S11.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

kruskal_wallis_P Q
ATP10D 2.341e-22 4.68e-18
C10ORF108 4.945e-21 2.64e-17
DIP2C 4.945e-21 2.64e-17
TMEM117 5.275e-21 2.64e-17
GPR87 1.142e-20 3.55e-17
MED12L__5 1.142e-20 3.55e-17
RGS12 1.417e-20 3.55e-17
HR 1.422e-20 3.55e-17
AKR1B10 3.213e-20 6.84e-17
BICD2 3.42e-20 6.84e-17
Clinical variable #8: 'NUMBER_PACK_YEARS_SMOKED'

No gene related to 'NUMBER_PACK_YEARS_SMOKED'.

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

NUMBER_PACK_YEARS_SMOKED Mean (SD) 17.38 (14)
  Significant markers N = 0
Clinical variable #9: 'NUMBER_OF_LYMPH_NODES'

30 genes related to 'NUMBER_OF_LYMPH_NODES'.

Table S13.  Basic characteristics of clinical feature: 'NUMBER_OF_LYMPH_NODES'

NUMBER_OF_LYMPH_NODES Mean (SD) 1.04 (2.4)
  Significant markers N = 30
  pos. correlated 22
  neg. correlated 8
List of top 10 genes differentially expressed by 'NUMBER_OF_LYMPH_NODES'

Table S14.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_OF_LYMPH_NODES' by Spearman correlation test

SpearmanCorr corrP Q
RCAN1 0.4028 1.412e-07 0.00282
NUAK1 0.3647 2.283e-06 0.0228
BCL9 0.3532 4.955e-06 0.033
ARIH2__1 0.3312 2e-05 0.08
C3ORF71__1 0.3312 2e-05 0.08
RNF20 -0.3266 2.653e-05 0.0804
PPARGC1A 0.3256 2.815e-05 0.0804
ZNF292 0.3203 3.845e-05 0.0882
DRAM1 0.3194 4.066e-05 0.0882
TXNDC6 0.3161 4.934e-05 0.0882
Clinical variable #10: 'RACE'

30 genes related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 8
  ASIAN 20
  BLACK OR AFRICAN AMERICAN 30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 2
  WHITE 211
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

Table S16.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
SNX16 7.794e-07 0.0156
PDXDC1 4.374e-06 0.0325
IFNGR2 4.881e-06 0.0325
TLE1 1.486e-05 0.0552
NDUFS5 1.536e-05 0.0552
FAM22A 2.258e-05 0.0552
RNF151 2.483e-05 0.0552
RPS2__3 2.483e-05 0.0552
SNHG9__2 2.483e-05 0.0552
HSD17B4 2.986e-05 0.0597
Clinical variable #11: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 24
  NOT HISPANIC OR LATINO 170
     
  Significant markers N = 0
Clinical variable #12: 'WEIGHT_KG_AT_DIAGNOSIS'

No gene related to 'WEIGHT_KG_AT_DIAGNOSIS'.

Table S18.  Basic characteristics of clinical feature: 'WEIGHT_KG_AT_DIAGNOSIS'

WEIGHT_KG_AT_DIAGNOSIS Mean (SD) 73.04 (22)
  Significant markers N = 0
Clinical variable #13: 'TUMOR_STATUS'

30 genes related to 'TUMOR_STATUS'.

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

TUMOR_STATUS Labels N
  TUMOR FREE 191
  WITH TUMOR 78
     
  Significant markers N = 30
  Higher in WITH TUMOR 30
  Higher in TUMOR FREE 0
List of top 10 genes differentially expressed by 'TUMOR_STATUS'

Table S20.  Get Full Table List of top 10 genes differentially expressed by 'TUMOR_STATUS'

W(pos if higher in 'WITH TUMOR') wilcoxontestP Q AUC
PATL2 10117 4.079e-06 0.0493 0.6791
CCR5 10094 4.933e-06 0.0493 0.6775
FAM35B2 4882 1.159e-05 0.0649 0.6706
CHRM3 4969 1.847e-05 0.0649 0.6665
MPDU1 9927 1.876e-05 0.0649 0.6663
SIT1 9883 2.632e-05 0.0649 0.6634
CD3D 9876 2.776e-05 0.0649 0.6629
GDAP1 5051 3.458e-05 0.0649 0.661
TIGIT 9827 4.018e-05 0.0649 0.6596
PSMD8 5064 4.714e-05 0.0649 0.6583
Clinical variable #14: 'NEOPLASM_HISTOLOGIC_GRADE'

30 genes related to 'NEOPLASM_HISTOLOGIC_GRADE'.

Table S21.  Basic characteristics of clinical feature: 'NEOPLASM_HISTOLOGIC_GRADE'

NEOPLASM_HISTOLOGIC_GRADE Labels N
  G1 18
  G2 136
  G3 120
  G4 1
  GX 24
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'NEOPLASM_HISTOLOGIC_GRADE'

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

kruskal_wallis_P Q
GMNN 3.108e-08 0.000621
MTF2 8.612e-08 0.000861
MRPS9 5.922e-07 0.00257
BRIX1__1 7.799e-07 0.00257
RAD1__1 7.799e-07 0.00257
PASK 8.989e-07 0.00257
PPP1R7 8.989e-07 0.00257
PAIP1 1.241e-06 0.0031
MYL6 1.525e-06 0.00339
C9ORF40 1.855e-06 0.00371
Clinical variable #15: '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) 1999.7 (14)
  Significant markers N = 0
Clinical variable #16: '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) 17.38 (14)
  Significant markers N = 0
Clinical variable #17: '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 40
  CURRENT REFORMED SMOKER FOR > 15 YEARS 9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED 4
  CURRENT SMOKER 64
  LIFELONG NON-SMOKER 146
     
  Significant markers N = 0
Clinical variable #18: 'AGEBEGANSMOKINGINYEARS'

No gene related to 'AGEBEGANSMOKINGINYEARS'.

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

AGEBEGANSMOKINGINYEARS Mean (SD) 21.14 (7.7)
  Significant markers N = 0
Clinical variable #19: 'RADIATION_THERAPY_STATUS'

No gene related to 'RADIATION_THERAPY_STATUS'.

Table S27.  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 #20: 'PREGNANCIES_COUNT_TOTAL'

No gene related to 'PREGNANCIES_COUNT_TOTAL'.

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

PREGNANCIES_COUNT_TOTAL Mean (SD) 3.61 (2.6)
  Significant markers N = 0
Clinical variable #21: 'PREGNANCIES_COUNT_STILLBIRTH'

No gene related to 'PREGNANCIES_COUNT_STILLBIRTH'.

Table S29.  Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_STILLBIRTH'

PREGNANCIES_COUNT_STILLBIRTH Mean (SD) 0.07 (0.35)
  Value N
  0 106
  1 5
  3 1
     
  Significant markers N = 0
Clinical variable #22: 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT'

30 genes related to 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT'.

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

PREGNANCY_SPONTANEOUS_ABORTION_COUNT Mean (SD) 0.54 (0.95)
  Significant markers N = 30
  pos. correlated 16
  neg. correlated 14
List of top 10 genes differentially expressed by 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT'

Table S31.  Get Full Table List of top 10 genes significantly correlated to 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT' by Spearman correlation test

SpearmanCorr corrP Q
GPRIN1 -0.4424 2.026e-08 0.000233
TAF3 0.4406 2.335e-08 0.000233
POLR2D 0.4234 9.105e-08 0.000607
C8ORF77 -0.4066 3.216e-07 0.00107
ZNF252 -0.4066 3.216e-07 0.00107
ZBTB1 -0.4026 4.295e-07 0.00107
ZBTB25 -0.4026 4.295e-07 0.00107
KNTC1 0.4036 4.8e-07 0.00107
RSRC2 0.4036 4.8e-07 0.00107
ZNF592 -0.3992 5.495e-07 0.0011
Clinical variable #23: 'PREGNANCIES_COUNT_LIVE_BIRTH'

30 genes related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

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

PREGNANCIES_COUNT_LIVE_BIRTH Mean (SD) 2.84 (2)
  Significant markers N = 30
  pos. correlated 12
  neg. correlated 18
List of top 10 genes differentially expressed by 'PREGNANCIES_COUNT_LIVE_BIRTH'

Table S33.  Get Full Table List of top 10 genes significantly correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH' by Spearman correlation test

SpearmanCorr corrP Q
POLE -0.3279 5.561e-08 0.000556
PXMP2 -0.3279 5.561e-08 0.000556
ZNF488 -0.3204 1.144e-07 0.000762
PALM3 -0.3126 2.532e-07 0.00127
PGF -0.2932 1.369e-06 0.00547
ZNF713 -0.2964 1.84e-06 0.00613
PDP2 -0.2861 2.515e-06 0.00718
LHX4 -0.2829 3.264e-06 0.00749
GPRIN1 -0.2826 3.371e-06 0.00749
HAUS8 -0.2778 4.991e-06 0.00813
Clinical variable #24: 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT'

No gene related to 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT'.

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

PREGNANCY_THERAPEUTIC_ABORTION_COUNT Mean (SD) 0.85 (1.8)
  Significant markers N = 0
Clinical variable #25: 'PREGNANCIES_COUNT_ECTOPIC'

No gene related to 'PREGNANCIES_COUNT_ECTOPIC'.

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

PREGNANCIES_COUNT_ECTOPIC Mean (SD) 0.11 (0.34)
  Value N
  0 104
  1 11
  2 1
     
  Significant markers N = 0
Clinical variable #26: 'POS_LYMPH_NODE_LOCATION'

No gene related to 'POS_LYMPH_NODE_LOCATION'.

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

POS_LYMPH_NODE_LOCATION Labels N
  MACROSCOPIC PARAMETRIAL INVOLVEMENT 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT 8
  OTHER LOCATION, SPECIFY 40
  POSITIVE BLADDER MARGIN 1
  POSITIVE VAGINAL MARGIN 10
     
  Significant markers N = 0
Clinical variable #27: 'MENOPAUSE_STATUS'

30 genes related to 'MENOPAUSE_STATUS'.

Table S37.  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) 25
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY) 84
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT) 125
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'MENOPAUSE_STATUS'

Table S38.  Get Full Table List of top 10 genes differentially expressed by 'MENOPAUSE_STATUS'

kruskal_wallis_P Q
C21ORF34 1.04e-06 0.00693
MIR99A 1.04e-06 0.00693
MIRLET7C 1.04e-06 0.00693
RARB 4.259e-06 0.0213
FBXW11 8.065e-06 0.0322
CMTM7 1.683e-05 0.0561
KCNC4 3.192e-05 0.0727
FBXO6 3.734e-05 0.0727
SMARCB1 4.238e-05 0.0727
CD9 4.668e-05 0.0727
Clinical variable #28: 'LYMPHOVASCULAR_INVOLVEMENT'

30 genes related to 'LYMPHOVASCULAR_INVOLVEMENT'.

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

LYMPHOVASCULAR_INVOLVEMENT Labels N
  ABSENT 72
  PRESENT 80
     
  Significant markers N = 30
  Higher in PRESENT 30
  Higher in ABSENT 0
List of top 10 genes differentially expressed by 'LYMPHOVASCULAR_INVOLVEMENT'

Clinical variable #29: 'LYMPH_NODES_EXAMINED_HE_COUNT'

30 genes related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

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

LYMPH_NODES_EXAMINED_HE_COUNT Mean (SD) 1.04 (2.4)
  Significant markers N = 30
  pos. correlated 22
  neg. correlated 8
List of top 10 genes differentially expressed by 'LYMPH_NODES_EXAMINED_HE_COUNT'

Table S42.  Get Full Table List of top 10 genes significantly correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT' by Spearman correlation test

SpearmanCorr corrP Q
RCAN1 0.4028 1.412e-07 0.00282
NUAK1 0.3647 2.283e-06 0.0228
BCL9 0.3532 4.955e-06 0.033
ARIH2__1 0.3312 2e-05 0.08
C3ORF71__1 0.3312 2e-05 0.08
RNF20 -0.3266 2.653e-05 0.0804
PPARGC1A 0.3256 2.815e-05 0.0804
ZNF292 0.3203 3.845e-05 0.0882
DRAM1 0.3194 4.066e-05 0.0882
TXNDC6 0.3161 4.934e-05 0.0882
Clinical variable #30: 'LYMPH_NODES_EXAMINED'

30 genes related to 'LYMPH_NODES_EXAMINED'.

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

LYMPH_NODES_EXAMINED Mean (SD) 22.28 (13)
  Significant markers N = 30
  pos. correlated 30
  neg. correlated 0
List of top 10 genes differentially expressed by 'LYMPH_NODES_EXAMINED'

Table S44.  Get Full Table List of top 10 genes significantly correlated to 'LYMPH_NODES_EXAMINED' by Spearman correlation test

SpearmanCorr corrP Q
LOC643837 0.3129 1.894e-05 0.259
HDAC1 0.2956 5.618e-05 0.259
NIPA1 0.2955 5.643e-05 0.259
TTLL10 0.2901 7.806e-05 0.259
CCDC134 0.2867 9.537e-05 0.259
ULK1 0.2862 9.803e-05 0.259
GAR1 0.2854 0.0001079 0.259
MPP2 0.2843 0.000115 0.259
SNORD1C 0.2812 0.0001311 0.259
DPH5 0.2797 0.0001428 0.259
Clinical variable #31: 'KERATINIZATION_SQUAMOUS_CELL'

No gene related to 'KERATINIZATION_SQUAMOUS_CELL'.

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

KERATINIZATION_SQUAMOUS_CELL Labels N
  KERATINIZING SQUAMOUS CELL CARCINOMA 55
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA 120
     
  Significant markers N = 0
Clinical variable #32: 'INITIAL_PATHOLOGIC_DX_YEAR'

30 genes related to 'INITIAL_PATHOLOGIC_DX_YEAR'.

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

INITIAL_PATHOLOGIC_DX_YEAR Mean (SD) 2008.32 (4.8)
  Significant markers N = 30
  pos. correlated 2
  neg. correlated 28
List of top 10 genes differentially expressed by 'INITIAL_PATHOLOGIC_DX_YEAR'

Table S47.  Get Full Table List of top 10 genes significantly correlated to 'INITIAL_PATHOLOGIC_DX_YEAR' by Spearman correlation test

SpearmanCorr corrP Q
KLHL9 0.3635 5.885e-11 4.89e-07
MMD -0.3628 6.409e-11 4.89e-07
RHOT2 -0.3617 7.343e-11 4.89e-07
DCDC1 -0.3525 2.365e-10 8.5e-07
DNAJC24 -0.3525 2.365e-10 8.5e-07
C9ORF44 -0.3519 2.551e-10 8.5e-07
HIST1H1E 0.3482 4.01e-10 9.26e-07
LOC285456 -0.3479 4.17e-10 9.26e-07
RPL34 -0.3479 4.17e-10 9.26e-07
MYLPF -0.3422 8.357e-10 1.67e-06
Clinical variable #33: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

No gene related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.

Table S48.  Basic characteristics of clinical feature: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

HISTORY_HORMONAL_CONTRACEPTIVES_USE Labels N
  CURRENT USER 15
  FORMER USER 54
  NEVER USED 90
     
  Significant markers N = 0
Clinical variable #34: 'HEIGHT_CM_AT_DIAGNOSIS'

No gene related to 'HEIGHT_CM_AT_DIAGNOSIS'.

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

HEIGHT_CM_AT_DIAGNOSIS Mean (SD) 160.95 (7.3)
  Significant markers N = 0
Clinical variable #35: 'CORPUS_INVOLVEMENT'

No gene related to 'CORPUS_INVOLVEMENT'.

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

CORPUS_INVOLVEMENT Labels N
  ABSENT 99
  PRESENT 19
     
  Significant markers N = 0
Clinical variable #36: 'CHEMO_CONCURRENT_TYPE'

No gene related to 'CHEMO_CONCURRENT_TYPE'.

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

CHEMO_CONCURRENT_TYPE Labels N
  CARBOPLATIN 7
  CISPLATIN 104
  OTHER 2
     
  Significant markers N = 0
Clinical variable #37: 'CERVIX_SUV_RESULTS'

No gene related to 'CERVIX_SUV_RESULTS'.

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

CERVIX_SUV_RESULTS Mean (SD) 13.22 (7.2)
  Significant markers N = 0
Clinical variable #38: 'AGE_AT_DIAGNOSIS'

30 genes related to 'AGE_AT_DIAGNOSIS'.

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

AGE_AT_DIAGNOSIS Mean (SD) 48.27 (14)
  Significant markers N = 30
  pos. correlated 10
  neg. correlated 20
List of top 10 genes differentially expressed by 'AGE_AT_DIAGNOSIS'

Table S54.  Get Full Table List of top 10 genes significantly correlated to 'AGE_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
C21ORF34 -0.3093 3.124e-08 0.000208
MIR99A -0.3093 3.124e-08 0.000208
MIRLET7C -0.3093 3.124e-08 0.000208
SP4 -0.3028 6.258e-08 0.000313
GLDC 0.2984 9.867e-08 0.000349
CHRNB1 0.2965 1.202e-07 0.000349
MDFI 0.2963 1.221e-07 0.000349
C10ORF67 0.2942 1.52e-07 0.00038
CCDC23 -0.2905 2.204e-07 0.000441
ERMAP -0.2905 2.204e-07 0.000441
Clinical variable #39: 'CLINICAL_STAGE'

30 genes related to 'CLINICAL_STAGE'.

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

CLINICAL_STAGE Labels N
  STAGE I 5
  STAGE IA 1
  STAGE IA1 1
  STAGE IA2 1
  STAGE IB 38
  STAGE IB1 78
  STAGE IB2 39
  STAGE II 5
  STAGE IIA 9
  STAGE IIA1 5
  STAGE IIA2 7
  STAGE IIB 44
  STAGE III 1
  STAGE IIIA 3
  STAGE IIIB 42
  STAGE IVA 9
  STAGE IVB 12
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'CLINICAL_STAGE'

Table S56.  Get Full Table List of top 10 genes differentially expressed by 'CLINICAL_STAGE'

kruskal_wallis_P Q
ARF4 8.113e-06 0.0375
C3ORF48 8.197e-06 0.0375
RAB5A 8.197e-06 0.0375
DPY30 8.729e-06 0.0375
ZNF322B 1.211e-05 0.0375
TMEM50A 1.319e-05 0.0375
PSMA3 1.41e-05 0.0375
WDR55 1.745e-05 0.0375
PDE1B 1.9e-05 0.0375
POU2F1 1.94e-05 0.0375
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 = 307

  • Number of genes = 19994

  • Number of clinical features = 39

Selected clinical features

  • Further details on clinical features selected for this analysis, please find a documentation on selected CDEs (Clinical Data Elements). The first column of the file is a formula to convert values and the second column is a clinical parameter name.

  • Survival time data

    • Survival time data is a combined value of days_to_death and days_to_last_followup. For each patient, it creates a combined value 'days_to_death_or_last_fup' using conversion process below.

      • if 'vital_status'==1(dead), 'days_to_last_followup' is always NA. Thus, uses 'days_to_death' value for 'days_to_death_or_fup'

      • if 'vital_status'==0(alive),

        • if 'days_to_death'==NA & 'days_to_last_followup'!=NA, uses 'days_to_last_followup' value for 'days_to_death_or_fup'

        • if 'days_to_death'!=NA, excludes this case in survival analysis and report the case.

      • if 'vital_status'==NA,excludes this case in survival analysis and report the case.

    • cf. In certain diesase types such as SKCM, days_to_death parameter is replaced with time_from_specimen_dx or time_from_specimen_procurement_to_death .

  • This analysis excluded clinical variables that has only NA values.

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

Wilcoxon rank sum test (Mann-Whitney U test)

For two groups (mutant or wild-type) of continuous type of clinical data, wilcoxon rank sum test (Mann and Whitney, 1947) was applied to compare their mean difference using 'wilcox.test(continuous.clinical ~ as.factor(group), exact=FALSE)' function in R. This test is equivalent to the Mann-Whitney test.

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] Mann and Whitney, On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other, Annals of Mathematical Statistics 18 (1), 50-60 (1947)
[4] 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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