Correlation between gene methylation status and clinical features
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1T43SFC
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene methylation status and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1T43SFC
Overview
Introduction

This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features. The input file "CESC-TP.meth.by_min_clin_corr.data.txt" is generated in the pipeline Methylation_Preprocess in stddata run.

Summary

Testing the association between 16894 genes and 39 clinical features across 307 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 19 clinical features related to at least one genes.

  • 6 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • BRD8 ,  C1ORF61 ,  FAM13A ,  FBLN5 ,  MED7 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • C21ORF34 ,  SP4 ,  GLDC ,  CHRNB1 ,  MDFI ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

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

  • 4 genes correlated to 'RADIATION_THERAPY'.

    • MGST2 ,  PDCL ,  PHF17 ,  HLA-DRB1

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • ATP10D ,  C10ORF108 ,  TMEM117 ,  GPR87 ,  RGS12 ,  ...

  • 30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

    • RCAN1 ,  NUAK1 ,  BCL9 ,  C3ORF71 ,  RNF20 ,  ...

  • 30 genes correlated to 'RACE'.

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

  • 30 genes correlated to 'TUMOR_STATUS'.

    • PATL2 ,  CCR5 ,  FAM35B2 ,  SIT1 ,  CHRM3 ,  ...

  • 30 genes correlated to 'NEOPLASM_HISTOLOGIC_GRADE'.

    • GMNN ,  MTF2 ,  MRPS9 ,  BRIX1 ,  PPP1R7 ,  ...

  • 4 genes correlated to 'TOBACCO_SMOKING_HISTORY'.

    • NKD2 ,  SCAP ,  QDPR ,  HPSE

  • 30 genes correlated to 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT'.

    • GPRIN1 ,  TAF3 ,  POLR2D ,  C8ORF77 ,  ZBTB25 ,  ...

  • 30 genes correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

    • POLE ,  ZNF488 ,  PALM3 ,  PGF ,  ZNF713 ,  ...

  • 30 genes correlated to 'MENOPAUSE_STATUS'.

    • C21ORF34 ,  CMTM7 ,  SALL3 ,  FBXW11 ,  RARB ,  ...

  • 30 genes correlated to 'LYMPHOVASCULAR_INVOLVEMENT'.

    • MKRN2 ,  ZNF197 ,  HYAL3 ,  TMEM87B ,  GAL3ST3 ,  ...

  • 30 genes correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

    • RCAN1 ,  NUAK1 ,  BCL9 ,  C3ORF71 ,  RNF20 ,  ...

  • 30 genes correlated to 'LYMPH_NODES_EXAMINED'.

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

  • 30 genes correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.

    • KLHL9 ,  MMD ,  RHOT2 ,  DCDC1 ,  C9ORF44 ,  ...

  • 30 genes correlated to 'AGE_AT_DIAGNOSIS'.

    • C21ORF34 ,  SP4 ,  GLDC ,  CHRNB1 ,  MDFI ,  ...

  • 30 genes correlated to 'CLINICAL_STAGE'.

    • ARF4 ,  C3ORF48 ,  DPY30 ,  ZNF322B ,  TMEM50A ,  ...

  • No genes correlated to 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'NUMBER_PACK_YEARS_SMOKED', 'ETHNICITY', 'WEIGHT_KG_AT_DIAGNOSIS', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_PACK_YEARS_SMOKED', '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=6   N=NA   N=NA
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=3 lower stage N=27
PATHOLOGY_N_STAGE Wilcoxon test   N=0        
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
RADIATION_THERAPY Wilcoxon test N=4 yes N=4 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=24 lower number_of_lymph_nodes N=6
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 Spearman correlation test N=4 higher tobacco_smoking_history N=3 lower tobacco_smoking_history N=1
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=10 lower pregnancies_count_live_birth N=20
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=24 lower lymph_nodes_examined_he_count N=6
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=11 lower age_at_diagnosis N=19
CLINICAL_STAGE Kruskal-Wallis test N=30        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

6 genes 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) 0.1-210.7 (median=23)
  censored N = 234
  death N = 72
     
  Significant markers N = 6
  associated with shorter survival NA
  associated with longer survival NA
List of 6 genes differentially expressed by 'DAYS_TO_DEATH_OR_LAST_FUP'

Table S2.  Get Full Table List of 6 genes significantly associated with 'Time to Death' by Cox regression test. For the survival curves, it compared quantile intervals at c(0, 0.25, 0.50, 0.75, 1) and did not try survival analysis if there is only one interval.

logrank_P Q C_index
BRD8 2.3e-05 0.27 0.607
C1ORF61 5.3e-05 0.27 0.451
FAM13A 7.93e-05 0.27 0.328
FBLN5 8.66e-05 0.27 0.655
MED7 8.96e-05 0.27 0.632
CABLES1 9.44e-05 0.27 0.584
Clinical variable #2: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

Table S3.  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 S4.  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 0.000331
SP4 -0.3061 4.887e-08 0.000331
GLDC 0.3022 7.377e-08 0.000331
CHRNB1 0.3016 7.846e-08 0.000331
MDFI 0.2987 1.051e-07 0.000355
ERMAP -0.2951 1.521e-07 0.000428
GALNT2 0.2927 1.947e-07 0.000435
RARB -0.2921 2.061e-07 0.000435
C10ORF67 0.2902 2.481e-07 0.000466
LOC100216001 -0.2879 3.11e-07 0.000525
Clinical variable #3: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

Table S5.  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 3
  neg. correlated 27
List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S6.  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 0.000144
NUP35 0.3443 3.371e-08 0.000144
PMCH -0.3443 3.378e-08 0.000144
MPP7 -0.343 3.828e-08 0.000144
DKFZP586I1420 -0.3426 4.265e-08 0.000144
NCOA2 -0.3418 6.745e-08 0.000171
ATP6AP1L -0.3366 7.096e-08 0.000171
TANC2 -0.3322 1.075e-07 0.000227
TMEM86B -0.3293 1.405e-07 0.000264
MIR155HG -0.3259 1.914e-07 0.000311
Clinical variable #4: 'PATHOLOGY_N_STAGE'

No gene related to 'PATHOLOGY_N_STAGE'.

Table S7.  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 S8.  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'

4 genes related to 'RADIATION_THERAPY'.

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

RADIATION_THERAPY Labels N
  NO 55
  YES 129
     
  Significant markers N = 4
  Higher in YES 4
  Higher in NO 0
List of 4 genes differentially expressed by 'RADIATION_THERAPY'

Table S10.  Get Full Table List of 4 genes differentially expressed by 'RADIATION_THERAPY'

W(pos if higher in 'YES') wilcoxontestP Q AUC
MGST2 5119 2.033e-06 0.0343 0.7215
PDCL 4989 1.318e-05 0.0753 0.7032
PHF17 4988 1.337e-05 0.0753 0.703
HLA-DRB1 4872 6.247e-05 0.264 0.6867
Clinical variable #7: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

Table S11.  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 S12.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

kruskal_wallis_P Q
ATP10D 2.341e-22 3.96e-18
C10ORF108 4.945e-21 2.97e-17
TMEM117 5.275e-21 2.97e-17
GPR87 1.142e-20 4e-17
RGS12 1.417e-20 4e-17
HR 1.422e-20 4e-17
AKR1B10 3.213e-20 7.22e-17
BICD2 3.42e-20 7.22e-17
DST 6.725e-20 1.26e-16
ARNTL2 9.374e-20 1.45e-16
Clinical variable #8: 'NUMBER_PACK_YEARS_SMOKED'

No gene related to 'NUMBER_PACK_YEARS_SMOKED'.

Table S13.  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 S14.  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 24
  neg. correlated 6
List of top 10 genes differentially expressed by 'NUMBER_OF_LYMPH_NODES'

Table S15.  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 0.00239
NUAK1 0.3647 2.283e-06 0.0193
BCL9 0.3532 4.955e-06 0.0279
C3ORF71 0.3312 2e-05 0.0793
RNF20 -0.3266 2.653e-05 0.0793
PPARGC1A 0.3256 2.815e-05 0.0793
ZNF292 0.3203 3.845e-05 0.0841
DRAM1 0.3194 4.066e-05 0.0841
TXNDC6 0.3161 4.934e-05 0.0841
ZNF572 0.3134 5.764e-05 0.0841
Clinical variable #10: 'RACE'

30 genes related to 'RACE'.

Table S16.  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 S17.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
SNX16 7.794e-07 0.0132
PDXDC1 4.374e-06 0.0275
IFNGR2 4.881e-06 0.0275
TLE1 1.486e-05 0.0519
NDUFS5 1.536e-05 0.0519
FAM22A 2.258e-05 0.0599
RNF151 2.483e-05 0.0599
HSD17B4 2.986e-05 0.0631
GPBAR1 3.821e-05 0.0701
FARSA 4.15e-05 0.0701
Clinical variable #11: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 24
  NOT HISPANIC OR LATINO 171
     
  Significant markers N = 0
Clinical variable #12: 'WEIGHT_KG_AT_DIAGNOSIS'

No gene related to 'WEIGHT_KG_AT_DIAGNOSIS'.

Table S19.  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 S20.  Basic characteristics of clinical feature: 'TUMOR_STATUS'

TUMOR_STATUS Labels N
  TUMOR FREE 201
  WITH TUMOR 80
     
  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 S21.  Get Full Table List of top 10 genes differentially expressed by 'TUMOR_STATUS'

W(pos if higher in 'WITH TUMOR') wilcoxontestP Q AUC
PATL2 10931 2.574e-06 0.0402 0.6798
CCR5 10806 6.834e-06 0.0402 0.672
FAM35B2 5297 1.01e-05 0.0402 0.6689
SIT1 10747 1.069e-05 0.0402 0.6683
CHRM3 5376 1.472e-05 0.0402 0.6657
TIGIT 10702 1.494e-05 0.0402 0.6655
GDAP1 5398 1.731e-05 0.0402 0.6643
FASLG 10669 1.903e-05 0.0402 0.6635
C6ORF134 5444 2.419e-05 0.0454 0.6614
MPDU1 10614 2.833e-05 0.0466 0.6601
Clinical variable #14: 'NEOPLASM_HISTOLOGIC_GRADE'

30 genes related to 'NEOPLASM_HISTOLOGIC_GRADE'.

Table S22.  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 S23.  Get Full Table List of top 10 genes differentially expressed by 'NEOPLASM_HISTOLOGIC_GRADE'

kruskal_wallis_P Q
GMNN 3.108e-08 0.000525
MTF2 8.612e-08 0.000727
MRPS9 5.922e-07 0.00304
BRIX1 7.799e-07 0.00304
PPP1R7 8.989e-07 0.00304
PAIP1 1.241e-06 0.0035
MYL6 1.525e-06 0.00368
C9ORF40 1.855e-06 0.00392
LSM5 2.129e-06 0.004
ATP5G1 2.965e-06 0.00501
Clinical variable #15: '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) 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 S25.  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'

4 genes related to 'TOBACCO_SMOKING_HISTORY'.

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

TOBACCO_SMOKING_HISTORY Mean (SD) 1.83 (1.1)
  Value N
  1 146
  2 64
  3 9
  4 40
  5 4
     
  Significant markers N = 4
  pos. correlated 3
  neg. correlated 1
List of 4 genes differentially expressed by 'TOBACCO_SMOKING_HISTORY'

Table S27.  Get Full Table List of 4 genes significantly correlated to 'TOBACCO_SMOKING_HISTORY' by Spearman correlation test

SpearmanCorr corrP Q
NKD2 -0.2599 1.97e-05 0.221
SCAP 0.2508 3.897e-05 0.221
QDPR 0.2494 4.31e-05 0.221
HPSE 0.2467 5.235e-05 0.221
Clinical variable #18: 'AGEBEGANSMOKINGINYEARS'

No gene related to 'AGEBEGANSMOKINGINYEARS'.

Table S28.  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 S29.  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 S30.  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 S31.  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 S32.  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 S33.  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 0.000197
TAF3 0.4406 2.335e-08 0.000197
POLR2D 0.4234 9.105e-08 0.000513
C8ORF77 -0.4066 3.216e-07 0.00133
ZBTB25 -0.4026 4.295e-07 0.00133
RSRC2 0.4036 4.8e-07 0.00133
ZNF592 -0.3992 5.495e-07 0.00133
ATL3 -0.3948 7.476e-07 0.00146
GOSR2 -0.3934 8.259e-07 0.00146
TRIM56 -0.3927 8.667e-07 0.00146
Clinical variable #23: 'PREGNANCIES_COUNT_LIVE_BIRTH'

30 genes related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

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

PREGNANCIES_COUNT_LIVE_BIRTH Mean (SD) 2.84 (2)
  Significant markers N = 30
  pos. correlated 10
  neg. correlated 20
List of top 10 genes differentially expressed by 'PREGNANCIES_COUNT_LIVE_BIRTH'

Table S35.  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 0.000939
ZNF488 -0.3204 1.144e-07 0.000966
PALM3 -0.3126 2.532e-07 0.00143
PGF -0.2932 1.369e-06 0.00578
ZNF713 -0.2964 1.84e-06 0.00622
PDP2 -0.2861 2.515e-06 0.00708
LHX4 -0.2829 3.264e-06 0.00712
GPRIN1 -0.2826 3.371e-06 0.00712
MYO9B -0.2778 4.991e-06 0.00862
NHEDC1 0.2769 5.376e-06 0.00862
Clinical variable #24: 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT'

No gene related to 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT'.

Table S36.  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 S37.  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 S38.  Basic characteristics of clinical feature: 'POS_LYMPH_NODE_LOCATION'

POS_LYMPH_NODE_LOCATION Labels N
  MACROSCOPIC PARAMETRIAL INVOLVEMENT 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT 8
  OTHER LOCATION, SPECIFY 40
  POSITIVE BLADDER MARGIN 1
  POSITIVE VAGINAL MARGIN 12
     
  Significant markers N = 0
Clinical variable #27: 'MENOPAUSE_STATUS'

30 genes related to 'MENOPAUSE_STATUS'.

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

MENOPAUSE_STATUS Labels N
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL) 3
  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 S40.  Get Full Table List of top 10 genes differentially expressed by 'MENOPAUSE_STATUS'

kruskal_wallis_P Q
C21ORF34 4.853e-06 0.082
CMTM7 2.168e-05 0.0831
SALL3 2.355e-05 0.0831
FBXW11 2.491e-05 0.0831
RARB 2.758e-05 0.0831
FLJ10213 2.951e-05 0.0831
CSGALNACT2 3.757e-05 0.0907
FBXO6 5.454e-05 0.11
MANBA 5.875e-05 0.11
SOX2 7.61e-05 0.124
Clinical variable #28: 'LYMPHOVASCULAR_INVOLVEMENT'

30 genes related to 'LYMPHOVASCULAR_INVOLVEMENT'.

Table S41.  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 S43.  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 24
  neg. correlated 6
List of top 10 genes differentially expressed by 'LYMPH_NODES_EXAMINED_HE_COUNT'

Table S44.  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 0.00239
NUAK1 0.3647 2.283e-06 0.0193
BCL9 0.3532 4.955e-06 0.0279
C3ORF71 0.3312 2e-05 0.0793
RNF20 -0.3266 2.653e-05 0.0793
PPARGC1A 0.3256 2.815e-05 0.0793
ZNF292 0.3203 3.845e-05 0.0841
DRAM1 0.3194 4.066e-05 0.0841
TXNDC6 0.3161 4.934e-05 0.0841
ZNF572 0.3134 5.764e-05 0.0841
Clinical variable #30: 'LYMPH_NODES_EXAMINED'

30 genes related to 'LYMPH_NODES_EXAMINED'.

Table S45.  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 S46.  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 0.239
HDAC1 0.2956 5.618e-05 0.239
NIPA1 0.2955 5.643e-05 0.239
TTLL10 0.2901 7.806e-05 0.239
CCDC134 0.2867 9.537e-05 0.239
ULK1 0.2862 9.803e-05 0.239
GAR1 0.2854 0.0001079 0.239
MPP2 0.2843 0.000115 0.239
SNORD1C 0.2812 0.0001311 0.239
DPH5 0.2797 0.0001428 0.239
Clinical variable #31: 'KERATINIZATION_SQUAMOUS_CELL'

No gene related to 'KERATINIZATION_SQUAMOUS_CELL'.

Table S47.  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 S48.  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 S49.  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 4.13e-07
MMD -0.3628 6.409e-11 4.13e-07
RHOT2 -0.3617 7.343e-11 4.13e-07
DCDC1 -0.3525 2.365e-10 8.62e-07
C9ORF44 -0.3519 2.551e-10 8.62e-07
HIST1H1E 0.3482 4.01e-10 1.01e-06
LOC285456 -0.3479 4.17e-10 1.01e-06
MYLPF -0.3422 8.357e-10 1.76e-06
TMEM86B -0.3402 1.062e-09 1.99e-06
RSPH3 -0.3389 1.244e-09 2.1e-06
Clinical variable #33: '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 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 S51.  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 S52.  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 S53.  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 S54.  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 S55.  Basic characteristics of clinical feature: 'AGE_AT_DIAGNOSIS'

AGE_AT_DIAGNOSIS Mean (SD) 48.27 (14)
  Significant markers N = 30
  pos. correlated 11
  neg. correlated 19
List of top 10 genes differentially expressed by 'AGE_AT_DIAGNOSIS'

Table S56.  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 0.000413
SP4 -0.3028 6.258e-08 0.000413
GLDC 0.2984 9.867e-08 0.000413
CHRNB1 0.2965 1.202e-07 0.000413
MDFI 0.2963 1.221e-07 0.000413
C10ORF67 0.2942 1.52e-07 0.000428
ERMAP -0.2905 2.204e-07 0.000532
RARB -0.2878 2.875e-07 0.000607
SERPINA1 0.284 4.186e-07 0.000783
GALNT2 0.2821 5.036e-07 0.000783
Clinical variable #39: 'CLINICAL_STAGE'

30 genes related to 'CLINICAL_STAGE'.

Table S57.  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 S58.  Get Full Table List of top 10 genes differentially expressed by 'CLINICAL_STAGE'

kruskal_wallis_P Q
ARF4 8.113e-06 0.0364
C3ORF48 8.197e-06 0.0364
DPY30 8.729e-06 0.0364
ZNF322B 1.211e-05 0.0364
TMEM50A 1.319e-05 0.0364
PSMA3 1.41e-05 0.0364
WDR55 1.745e-05 0.0364
PDE1B 1.9e-05 0.0364
POU2F1 1.94e-05 0.0364
AFARP1 2.417e-05 0.0403
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 = 16894

  • 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, logrank test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values comparing quantile intervals using the 'coxph' function in R. Kaplan-Meier survival curves were plotted using quantile intervals at c(0, 0.25, 0.50, 0.75, 1). If there is only one interval group, it will not try survival analysis.

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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