Correlation between mutation rate and clinical features
Overview
Introduction

This pipeline uses various statistical tests to identify selected clinical features related to mutation rate.

Summary

Testing the association between 2 variables and 40 clinical features across 194 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 8 clinical features related to at least one variables.

  • 2 variables correlated to 'AGE'.

    • MUTATIONRATE_SILENT ,  MUTATIONRATE_NONSYNONYMOUS

  • 2 variables correlated to 'AGE_mutation.rate'.

    • MUTATIONRATE_NONSYNONYMOUS ,  MUTATIONRATE_SILENT

  • 2 variables correlated to 'NUMBER_PACK_YEARS_SMOKED'.

    • MUTATIONRATE_NONSYNONYMOUS ,  MUTATIONRATE_SILENT

  • 2 variables correlated to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.

    • MUTATIONRATE_NONSYNONYMOUS ,  MUTATIONRATE_SILENT

  • 2 variables correlated to 'MENOPAUSE_STATUS'.

    • MUTATIONRATE_SILENT ,  MUTATIONRATE_NONSYNONYMOUS

  • 1 variable correlated to 'KERATINIZATION_SQUAMOUS_CELL'.

    • MUTATIONRATE_SILENT

  • 1 variable correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.

    • MUTATIONRATE_SILENT

  • 2 variables correlated to 'AGE_AT_DIAGNOSIS'.

    • MUTATIONRATE_SILENT ,  MUTATIONRATE_NONSYNONYMOUS

  • No variables correlated to 'DAYS_TO_DEATH_OR_LAST_FUP', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', 'RACE', 'ETHNICITY', 'WEIGHT_KG_AT_DIAGNOSIS', 'TUMOR_STATUS', 'NEOPLASM_HISTOLOGIC_GRADE', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_HISTORY', 'AGEBEGANSMOKINGINYEARS', 'RADIATION_THERAPY_STATUS', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT', 'PREGNANCIES_COUNT_LIVE_BIRTH', 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT', 'PREGNANCIES_COUNT_ECTOPIC', 'POS_LYMPH_NODE_LOCATION', 'LYMPHOVASCULAR_INVOLVEMENT', 'LYMPH_NODES_EXAMINED_HE_COUNT', 'LYMPH_NODES_EXAMINED', 'HISTORY_HORMONAL_CONTRACEPTIVES_USE', 'HEIGHT_CM_AT_DIAGNOSIS', 'CORPUS_INVOLVEMENT', 'CHEMO_CONCURRENT_TYPE', 'CERVIX_SUV_RESULTS', and '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 variables that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.

Clinical feature Statistical test Significant variables Associated with                 Associated with
DAYS_TO_DEATH_OR_LAST_FUP Cox regression test   N=0        
AGE Spearman correlation test N=2 older N=2 younger N=0
AGE Linear Regression Analysis N=2        
PATHOLOGY_T_STAGE Spearman correlation test   N=0        
PATHOLOGY_N_STAGE Wilcoxon test   N=0        
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
RADIATION_THERAPY Wilcoxon test   N=0        
HISTOLOGICAL_TYPE Kruskal-Wallis test   N=0        
NUMBER_PACK_YEARS_SMOKED Spearman correlation test N=2 higher number_pack_years_smoked N=2 lower number_pack_years_smoked N=0
NUMBER_OF_LYMPH_NODES Spearman correlation test   N=0        
RACE Kruskal-Wallis test   N=0        
ETHNICITY Wilcoxon test   N=0        
WEIGHT_KG_AT_DIAGNOSIS Spearman correlation test   N=0        
TUMOR_STATUS Wilcoxon test   N=0        
NEOPLASM_HISTOLOGIC_GRADE Kruskal-Wallis test   N=0        
TOBACCO_SMOKING_YEAR_STOPPED Spearman correlation test   N=0        
TOBACCO_SMOKING_PACK_YEARS_SMOKED Spearman correlation test N=2 higher tobacco_smoking_pack_years_smoked N=2 lower tobacco_smoking_pack_years_smoked N=0
TOBACCO_SMOKING_HISTORY Spearman correlation 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=0        
PREGNANCIES_COUNT_LIVE_BIRTH Spearman correlation test   N=0        
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=2        
LYMPHOVASCULAR_INVOLVEMENT Wilcoxon test   N=0        
LYMPH_NODES_EXAMINED_HE_COUNT Spearman correlation test   N=0        
LYMPH_NODES_EXAMINED Spearman correlation test   N=0        
KERATINIZATION_SQUAMOUS_CELL Wilcoxon test N=1 non-keratinizing squamous cell carcinoma N=1 keratinizing squamous cell carcinoma N=0
INITIAL_PATHOLOGIC_DX_YEAR Spearman correlation test N=1 higher initial_pathologic_dx_year N=0 lower initial_pathologic_dx_year N=1
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=2 higher age_at_diagnosis N=2 lower age_at_diagnosis N=0
CLINICAL_STAGE Kruskal-Wallis test   N=0        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

No variable 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=23.8)
  censored N = 151
  death N = 42
     
  Significant variables N = 0
Clinical variable #2: 'AGE'

2 variables related to 'AGE'.

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

AGE Mean (SD) 47.29 (13)
  Significant variables N = 2
  pos. correlated 2
  neg. correlated 0
List of 2 variables associated with 'AGE'

Table S3.  Get Full Table List of 2 variables significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
MUTATIONRATE_SILENT 0.3242 4.481e-06 8.96e-06
MUTATIONRATE_NONSYNONYMOUS 0.314 9.175e-06 9.17e-06
Clinical variable #3: 'AGE'

2 variables related to 'AGE'.

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

AGE Mean (SD) 47.29 (13)
  Significant variables N = 2
List of 2 variables associated with 'AGE'

Table S5.  Get Full Table List of 2 variables significantly correlated to 'AGE' by Linear regression analysis [lm (mutation rate ~ age)]. Compared to a correlation analysis testing for interdependence of the variables, a regression model attempts to describe the dependence of a variable on one (or more) explanatory variables assuming that there is a one-way causal effect from the explanatory variable(s) to the response variable. If 'Residuals vs Fitted' plot (a standard residual plot) shows a random pattern indicating a good fit for a linear model, it explains linear regression relationship between Mutation rate and age factor. Adj.R-squared (= Explained variation / Total variation) indicates regression model's explanatory power.

Adj.R.squared F P Residual.std.err DF coef(intercept) coef.p(intercept)
MUTATIONRATE_NONSYNONYMOUS 0.0236 5.61 0.0189 7.13e-06 190 9.23e-08 ( -3.38e-07 ) 0.0189 ( 0.86 )
MUTATIONRATE_SILENT 0.0225 5.39 0.0213 2.08e-06 190 2.64e-08 ( 1.24e-08 ) 0.0213 ( 0.982 )
Clinical variable #4: 'PATHOLOGY_T_STAGE'

No variable related to 'PATHOLOGY_T_STAGE'.

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

PATHOLOGY_T_STAGE Mean (SD) 1.35 (0.59)
  N
  T1 104
  T2 40
  T3 3
  T4 2
     
  Significant variables N = 0
Clinical variable #5: 'PATHOLOGY_N_STAGE'

No variable related to 'PATHOLOGY_N_STAGE'.

Table S7.  Basic characteristics of clinical feature: 'PATHOLOGY_N_STAGE'

PATHOLOGY_N_STAGE Labels N
  N0 95
  N1 44
     
  Significant variables N = 0
Clinical variable #6: 'PATHOLOGY_M_STAGE'

No variable related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 79
  class1 4
     
  Significant variables N = 0
Clinical variable #7: 'RADIATION_THERAPY'

No variable related to 'RADIATION_THERAPY'.

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

RADIATION_THERAPY Labels N
  NO 40
  YES 52
     
  Significant variables N = 0
Clinical variable #8: 'HISTOLOGICAL_TYPE'

No variable related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  ADENOSQUAMOUS 4
  CERVICAL SQUAMOUS CELL CARCINOMA 158
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA 21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE 4
     
  Significant variables N = 0
Clinical variable #9: 'NUMBER_PACK_YEARS_SMOKED'

2 variables related to 'NUMBER_PACK_YEARS_SMOKED'.

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

NUMBER_PACK_YEARS_SMOKED Mean (SD) 18.65 (12)
  Significant variables N = 2
  pos. correlated 2
  neg. correlated 0
List of 2 variables associated with 'NUMBER_PACK_YEARS_SMOKED'

Table S12.  Get Full Table List of 2 variables significantly correlated to 'NUMBER_PACK_YEARS_SMOKED' by Spearman correlation test

SpearmanCorr corrP Q
MUTATIONRATE_NONSYNONYMOUS 0.3788 0.003666 0.00733
MUTATIONRATE_SILENT 0.3446 0.008671 0.00867
Clinical variable #10: 'NUMBER_OF_LYMPH_NODES'

No variable related to 'NUMBER_OF_LYMPH_NODES'.

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

NUMBER_OF_LYMPH_NODES Mean (SD) 1.02 (2.2)
  Significant variables N = 0
Clinical variable #11: 'RACE'

No variable 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 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 1
  WHITE 138
     
  Significant variables N = 0
Clinical variable #12: 'ETHNICITY'

No variable related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 14
  NOT HISPANIC OR LATINO 135
     
  Significant variables N = 0
Clinical variable #13: 'WEIGHT_KG_AT_DIAGNOSIS'

No variable related to 'WEIGHT_KG_AT_DIAGNOSIS'.

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

WEIGHT_KG_AT_DIAGNOSIS Mean (SD) 75.87 (22)
  Significant variables N = 0
Clinical variable #14: 'TUMOR_STATUS'

No variable related to 'TUMOR_STATUS'.

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

TUMOR_STATUS Labels N
  TUMOR FREE 139
  WITH TUMOR 45
     
  Significant variables N = 0
Clinical variable #15: 'NEOPLASM_HISTOLOGIC_GRADE'

No variable related to 'NEOPLASM_HISTOLOGIC_GRADE'.

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

NEOPLASM_HISTOLOGIC_GRADE Labels N
  G1 14
  G2 88
  G3 82
  G4 1
  GX 8
     
  Significant variables N = 0
Clinical variable #16: 'TOBACCO_SMOKING_YEAR_STOPPED'

No variable related to 'TOBACCO_SMOKING_YEAR_STOPPED'.

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

TOBACCO_SMOKING_YEAR_STOPPED Mean (SD) 1998.93 (12)
  Significant variables N = 0
Clinical variable #17: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'

2 variables related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.

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

TOBACCO_SMOKING_PACK_YEARS_SMOKED Mean (SD) 18.65 (12)
  Significant variables N = 2
  pos. correlated 2
  neg. correlated 0
List of 2 variables associated with 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'

Table S21.  Get Full Table List of 2 variables significantly correlated to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED' by Spearman correlation test

SpearmanCorr corrP Q
MUTATIONRATE_NONSYNONYMOUS 0.3788 0.003666 0.00733
MUTATIONRATE_SILENT 0.3446 0.008671 0.00867
Clinical variable #18: 'TOBACCO_SMOKING_HISTORY'

No variable related to 'TOBACCO_SMOKING_HISTORY'.

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

TOBACCO_SMOKING_HISTORY Mean (SD) 1.82 (1.1)
  Value N
  1 93
  2 37
  3 8
  4 26
  5 1
     
  Significant variables N = 0
Clinical variable #19: 'AGEBEGANSMOKINGINYEARS'

No variable related to 'AGEBEGANSMOKINGINYEARS'.

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

AGEBEGANSMOKINGINYEARS Mean (SD) 21.37 (7.4)
  Significant variables N = 0
Clinical variable #20: 'RADIATION_THERAPY_STATUS'

No variable related to 'RADIATION_THERAPY_STATUS'.

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

RADIATION_THERAPY_STATUS Labels N
  COMPLETED AS PLANNED 26
  TREATMENT NOT COMPLETED 3
     
  Significant variables N = 0
Clinical variable #21: 'PREGNANCIES_COUNT_TOTAL'

No variable related to 'PREGNANCIES_COUNT_TOTAL'.

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

PREGNANCIES_COUNT_TOTAL Mean (SD) 3.41 (2.4)
  Significant variables N = 0
Clinical variable #22: 'PREGNANCIES_COUNT_STILLBIRTH'

No variable related to 'PREGNANCIES_COUNT_STILLBIRTH'.

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

PREGNANCIES_COUNT_STILLBIRTH Mean (SD) 0.08 (0.37)
  Value N
  0 95
  1 5
  3 1
     
  Significant variables N = 0
Clinical variable #23: 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT'

No variable related to 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT'.

Table S27.  Basic characteristics of clinical feature: 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT'

PREGNANCY_SPONTANEOUS_ABORTION_COUNT Mean (SD) 0.31 (0.57)
  Value N
  0 81
  1 25
  2 3
  3 1
     
  Significant variables N = 0
Clinical variable #24: 'PREGNANCIES_COUNT_LIVE_BIRTH'

No variable related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

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

PREGNANCIES_COUNT_LIVE_BIRTH Mean (SD) 2.4 (1.7)
  Significant variables N = 0
Clinical variable #25: 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT'

No variable related to 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT'.

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

PREGNANCY_THERAPEUTIC_ABORTION_COUNT Mean (SD) 0.88 (1.9)
  Significant variables N = 0
Clinical variable #26: 'PREGNANCIES_COUNT_ECTOPIC'

No variable related to 'PREGNANCIES_COUNT_ECTOPIC'.

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

PREGNANCIES_COUNT_ECTOPIC Mean (SD) 0.11 (0.34)
  Value N
  0 93
  1 9
  2 1
     
  Significant variables N = 0
Clinical variable #27: 'POS_LYMPH_NODE_LOCATION'

No variable related to 'POS_LYMPH_NODE_LOCATION'.

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

POS_LYMPH_NODE_LOCATION Labels N
  MACROSCOPIC PARAMETRIAL INVOLVEMENT 1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT 7
  OTHER LOCATION, SPECIFY 30
  POSITIVE BLADDER MARGIN 1
  POSITIVE VAGINAL MARGIN 8
     
  Significant variables N = 0
Clinical variable #28: 'MENOPAUSE_STATUS'

2 variables related to 'MENOPAUSE_STATUS'.

Table S32.  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) 10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY) 60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT) 88
     
  Significant variables N = 2
List of 2 variables associated with 'MENOPAUSE_STATUS'

Table S33.  Get Full Table List of 2 variables differentially expressed by 'MENOPAUSE_STATUS'

kruskal_wallis_P Q
MUTATIONRATE_SILENT 4.944e-05 9.89e-05
MUTATIONRATE_NONSYNONYMOUS 0.0007629 0.000763
Clinical variable #29: 'LYMPHOVASCULAR_INVOLVEMENT'

No variable related to 'LYMPHOVASCULAR_INVOLVEMENT'.

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

LYMPHOVASCULAR_INVOLVEMENT Labels N
  ABSENT 63
  PRESENT 67
     
  Significant variables N = 0
Clinical variable #30: 'LYMPH_NODES_EXAMINED_HE_COUNT'

No variable related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

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

LYMPH_NODES_EXAMINED_HE_COUNT Mean (SD) 1.02 (2.2)
  Significant variables N = 0
Clinical variable #31: 'LYMPH_NODES_EXAMINED'

No variable related to 'LYMPH_NODES_EXAMINED'.

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

LYMPH_NODES_EXAMINED Mean (SD) 21.56 (13)
  Significant variables N = 0
Clinical variable #32: 'KERATINIZATION_SQUAMOUS_CELL'

One variable related to 'KERATINIZATION_SQUAMOUS_CELL'.

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

KERATINIZATION_SQUAMOUS_CELL Labels N
  KERATINIZING SQUAMOUS CELL CARCINOMA 39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA 86
     
  Significant variables N = 1
  Higher in NON-KERATINIZING SQUAMOUS CELL CARCINOMA 1
  Higher in KERATINIZING SQUAMOUS CELL CARCINOMA 0
List of one variable associated with 'KERATINIZATION_SQUAMOUS_CELL'

Table S38.  Get Full Table List of one variable differentially expressed by 'KERATINIZATION_SQUAMOUS_CELL'

W(pos if higher in 'NON-KERATINIZING SQUAMOUS CELL CARCINOMA') wilcoxontestP Q AUC
MUTATIONRATE_SILENT 1290.5 0.03964 0.0773 0.6152
Clinical variable #33: 'INITIAL_PATHOLOGIC_DX_YEAR'

One variable related to 'INITIAL_PATHOLOGIC_DX_YEAR'.

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

INITIAL_PATHOLOGIC_DX_YEAR Mean (SD) 2007.66 (5.1)
  Significant variables N = 1
  pos. correlated 0
  neg. correlated 1
List of one variable associated with 'INITIAL_PATHOLOGIC_DX_YEAR'

Table S40.  Get Full Table List of one variable significantly correlated to 'INITIAL_PATHOLOGIC_DX_YEAR' by Spearman correlation test

SpearmanCorr corrP Q
MUTATIONRATE_SILENT -0.1498 0.03805 0.0656
Clinical variable #34: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

No variable related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.

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

HISTORY_HORMONAL_CONTRACEPTIVES_USE Labels N
  CURRENT USER 8
  FORMER USER 43
  NEVER USED 46
     
  Significant variables N = 0
Clinical variable #35: 'HEIGHT_CM_AT_DIAGNOSIS'

No variable related to 'HEIGHT_CM_AT_DIAGNOSIS'.

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

HEIGHT_CM_AT_DIAGNOSIS Mean (SD) 162.15 (6.6)
  Significant variables N = 0
Clinical variable #36: 'CORPUS_INVOLVEMENT'

No variable related to 'CORPUS_INVOLVEMENT'.

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

CORPUS_INVOLVEMENT Labels N
  ABSENT 88
  PRESENT 16
     
  Significant variables N = 0
Clinical variable #37: 'CHEMO_CONCURRENT_TYPE'

No variable related to 'CHEMO_CONCURRENT_TYPE'.

Table S44.  Basic characteristics of clinical feature: 'CHEMO_CONCURRENT_TYPE'

CHEMO_CONCURRENT_TYPE Labels N
  CARBOPLATIN 4
  CISPLATIN 53
  OTHER 1
     
  Significant variables N = 0
Clinical variable #38: 'CERVIX_SUV_RESULTS'

No variable related to 'CERVIX_SUV_RESULTS'.

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

CERVIX_SUV_RESULTS Mean (SD) 11.79 (3.8)
  Significant variables N = 0
Clinical variable #39: 'AGE_AT_DIAGNOSIS'

2 variables related to 'AGE_AT_DIAGNOSIS'.

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

AGE_AT_DIAGNOSIS Mean (SD) 47.42 (13)
  Significant variables N = 2
  pos. correlated 2
  neg. correlated 0
List of 2 variables associated with 'AGE_AT_DIAGNOSIS'

Table S47.  Get Full Table List of 2 variables significantly correlated to 'AGE_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
MUTATIONRATE_SILENT 0.3308 2.459e-06 4.82e-06
MUTATIONRATE_NONSYNONYMOUS 0.3216 4.823e-06 4.82e-06
Clinical variable #40: 'CLINICAL_STAGE'

No variable related to 'CLINICAL_STAGE'.

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

CLINICAL_STAGE Labels N
  STAGE I 4
  STAGE IA 1
  STAGE IA1 1
  STAGE IA2 1
  STAGE IB 28
  STAGE IB1 53
  STAGE IB2 29
  STAGE II 4
  STAGE IIA 6
  STAGE IIA1 5
  STAGE IIA2 7
  STAGE IIB 14
  STAGE III 1
  STAGE IIIB 29
  STAGE IVA 2
  STAGE IVB 5
     
  Significant variables N = 0
Methods & Data
Input

  • Expresson data file = CESC-TP.patients.counts_and_rates.txt

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

  • Number of patients = 194

  • Number of variables = 2

  • Number of clinical features = 40

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.

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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