Correlation between mutation rate and clinical features
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1MK6BQB
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between mutation rate and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1MK6BQB
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 45 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 'NUMBERPACKYEARSSMOKED'.

    • MUTATIONRATE_SILENT ,  MUTATIONRATE_NONSYNONYMOUS

  • 2 variables correlated to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.

    • MUTATIONRATE_SILENT ,  MUTATIONRATE_NONSYNONYMOUS

  • 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 'Time to Death', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'HISTOLOGICAL.TYPE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'NUMBER.OF.LYMPH.NODES', 'RACE', 'ETHNICITY', 'WEIGHT_KG_AT_DIAGNOSIS', 'TUMOR_STATUS', 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY', 'NEOPLASMHISTOLOGICGRADE', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_HISTORY', 'PATIENT.AGEBEGANSMOKINGINYEARS', 'RADIATION_TOTAL_DOSE', 'RADIATION_THERAPY_TYPE', 'RADIATION_THERAPY_STATUS', 'RADIATION_THERAPY_SITE', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT', 'PREGNANCIES_COUNT_LIVE_BIRTH', 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT', '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', 'AJCC_TUMOR_PATHOLOGIC_PT', and 'STAGE_EVENT.CLINICAL_STAGE'.

Results
Overview of the results

Complete statistical result table is provided in Supplement Table 1

Table 1.  Get Full Table This table shows the clinical features, statistical methods used, and the number of 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
Time to Death 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 Kruskal-Wallis test   N=0        
HISTOLOGICAL TYPE Kruskal-Wallis test   N=0        
RADIATIONS RADIATION REGIMENINDICATION Wilcoxon test   N=0        
NUMBERPACKYEARSSMOKED Spearman correlation test N=2 higher numberpackyearssmoked N=2 lower numberpackyearssmoked 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        
TUMOR_SAMPLE_PROCUREMENT_COUNTRY Kruskal-Wallis test   N=0        
NEOPLASMHISTOLOGICGRADE 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 Kruskal-Wallis test   N=0        
PATIENT AGEBEGANSMOKINGINYEARS Spearman correlation test   N=0        
RADIATION_TOTAL_DOSE Spearman correlation test   N=0        
RADIATION_THERAPY_TYPE Kruskal-Wallis test   N=0        
RADIATION_THERAPY_STATUS Wilcoxon test   N=0        
RADIATION_THERAPY_SITE Kruskal-Wallis 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=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        
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        
AJCC_TUMOR_PATHOLOGIC_PT Kruskal-Wallis test   N=0        
AGE_AT_DIAGNOSIS Spearman correlation test N=2 higher age_at_diagnosis N=2 lower age_at_diagnosis N=0
STAGE_EVENT CLINICAL_STAGE Kruskal-Wallis test   N=0        
Clinical variable #1: 'Time to Death'

No variable related to 'Time to Death'.

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

Time to Death Duration (Months) 0-195.8 (median=15)
  censored N = 152
  death N = 37
     
  Significant variables N = 0
Clinical variable #2: 'AGE'

2 variables related to 'AGE'.

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

AGE Mean (SD) 47.25 (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 0.3366 2.048e-06 4.1e-06
MUTATIONRATE_NONSYNONYMOUS 0.3308 3.145e-06 4.1e-06
Clinical variable #3: 'AGE'

2 variables related to 'AGE'.

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

AGE Mean (SD) 47.25 (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 0.0244 5.73 0.0177 8.05e-06 188 1.05e-07 ( -3.02e-07 ) 0.0177 ( 0.889 )
MUTATIONRATE_SILENT 0.0242 5.69 0.018 2.4e-06 188 3.13e-08 ( 2.25e-08 ) 0.018 ( 0.972 )
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) 1.34 (0.59)
  N
  1 106
  2 40
  3 3
  4 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
  class0 95
  class1 46
     
  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
  M0 81
  M1 4
  MX 70
     
  Significant variables N = 0
Clinical variable #7: 'HISTOLOGICAL.TYPE'

No variable related to 'HISTOLOGICAL.TYPE'.

Table S9.  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 22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE 3
     
  Significant variables N = 0
Clinical variable #8: 'RADIATIONS.RADIATION.REGIMENINDICATION'

No variable related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

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

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 32
  YES 162
     
  Significant variables N = 0
Clinical variable #9: 'NUMBERPACKYEARSSMOKED'

2 variables related to 'NUMBERPACKYEARSSMOKED'.

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

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

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

SpearmanCorr corrP Q
MUTATIONRATE_SILENT 0.4256 0.000964 0.00193
MUTATIONRATE_NONSYNONYMOUS 0.3829 0.003282 0.00328
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 134
     
  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) 75.98 (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 72
  WITH TUMOR 26
     
  Significant variables N = 0
Clinical variable #15: 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

No variable related to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.

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

TUMOR_SAMPLE_PROCUREMENT_COUNTRY Labels N
  CANADA 5
  RUSSIA 10
  UKRAINE 6
  UNITED STATES 159
  VIETNAM 14
     
  Significant variables N = 0
Clinical variable #16: 'NEOPLASMHISTOLOGICGRADE'

No variable related to 'NEOPLASMHISTOLOGICGRADE'.

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

NEOPLASMHISTOLOGICGRADE Labels N
  G1 14
  G2 88
  G3 82
  G4 1
  GX 8
     
  Significant variables N = 0
Clinical variable #17: 'TOBACCO_SMOKING_YEAR_STOPPED'

No variable related to 'TOBACCO_SMOKING_YEAR_STOPPED'.

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

TOBACCO_SMOKING_YEAR_STOPPED Mean (SD) 1998.93 (12)
  Significant variables N = 0
Clinical variable #18: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'

2 variables related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.

Table S21.  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 S22.  Get Full Table List of 2 variables significantly correlated to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED' by Spearman correlation test

SpearmanCorr corrP Q
MUTATIONRATE_SILENT 0.4256 0.000964 0.00193
MUTATIONRATE_NONSYNONYMOUS 0.3829 0.003282 0.00328
Clinical variable #19: 'TOBACCO_SMOKING_HISTORY'

No variable related to 'TOBACCO_SMOKING_HISTORY'.

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

TOBACCO_SMOKING_HISTORY Labels N
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS 26
  CURRENT REFORMED SMOKER FOR > 15 YEARS 8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED 1
  CURRENT SMOKER 37
  LIFELONG NON-SMOKER 92
     
  Significant variables N = 0
Clinical variable #20: 'PATIENT.AGEBEGANSMOKINGINYEARS'

No variable related to 'PATIENT.AGEBEGANSMOKINGINYEARS'.

Table S24.  Basic characteristics of clinical feature: 'PATIENT.AGEBEGANSMOKINGINYEARS'

PATIENT.AGEBEGANSMOKINGINYEARS Mean (SD) 21.37 (7.4)
  Significant variables N = 0
Clinical variable #21: 'RADIATION_TOTAL_DOSE'

No variable related to 'RADIATION_TOTAL_DOSE'.

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

RADIATION_TOTAL_DOSE Mean (SD) 3863.29 (1700)
  Significant variables N = 0
Clinical variable #22: 'RADIATION_THERAPY_TYPE'

No variable related to 'RADIATION_THERAPY_TYPE'.

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

RADIATION_THERAPY_TYPE Labels N
  COMBINATION 20
  EXTERNAL 45
  EXTERNAL BEAM 12
  IMPLANTS 1
  INTERNAL 6
     
  Significant variables N = 0
Clinical variable #23: 'RADIATION_THERAPY_STATUS'

No variable related to 'RADIATION_THERAPY_STATUS'.

Table S27.  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 #24: 'RADIATION_THERAPY_SITE'

No variable related to 'RADIATION_THERAPY_SITE'.

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

RADIATION_THERAPY_SITE Labels N
  DISTANT RECURRENCE 2
  LOCAL RECURRENCE 2
  PRIMARY TUMOR FIELD 15
  REGIONAL SITE 3
     
  Significant variables N = 0
Clinical variable #25: 'PREGNANCIES_COUNT_TOTAL'

No variable related to 'PREGNANCIES_COUNT_TOTAL'.

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

PREGNANCIES_COUNT_TOTAL Mean (SD) 3.41 (2.4)
  Significant variables N = 0
Clinical variable #26: 'PREGNANCIES_COUNT_STILLBIRTH'

No variable related to 'PREGNANCIES_COUNT_STILLBIRTH'.

Table S30.  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 #27: 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

No variable related to 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.

Table S31.  Basic characteristics of clinical feature: 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT Mean (SD) 0.31 (0.57)
  Value N
  0 81
  1 25
  2 3
  3 1
     
  Significant variables N = 0
Clinical variable #28: 'PREGNANCIES_COUNT_LIVE_BIRTH'

No variable related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

Table S32.  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 #29: 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

No variable related to 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.

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

PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT Mean (SD) 0.88 (1.9)
  Significant variables N = 0
Clinical variable #30: 'PREGNANCIES_COUNT_ECTOPIC'

No variable related to 'PREGNANCIES_COUNT_ECTOPIC'.

Table S34.  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 #31: 'POS_LYMPH_NODE_LOCATION'

No variable related to 'POS_LYMPH_NODE_LOCATION'.

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

POS_LYMPH_NODE_LOCATION Labels N
  MACROSCOPIC PARAMETRIAL INVOLVEMENT 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT 6
  OTHER LOCATION, SPECIFY 26
  POSITIVE BLADDER MARGIN 1
  POSITIVE VAGINAL MARGIN 6
     
  Significant variables N = 0
Clinical variable #32: 'MENOPAUSE_STATUS'

2 variables related to 'MENOPAUSE_STATUS'.

Table S36.  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) 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 S37.  Get Full Table List of 2 variables differentially expressed by 'MENOPAUSE_STATUS'

ANOVA_P Q
MUTATIONRATE_SILENT 6.626e-05 0.000133
MUTATIONRATE_NONSYNONYMOUS 0.0007806 0.000781
Clinical variable #33: 'LYMPHOVASCULAR_INVOLVEMENT'

No variable related to 'LYMPHOVASCULAR_INVOLVEMENT'.

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

LYMPHOVASCULAR_INVOLVEMENT Labels N
  ABSENT 63
  PRESENT 67
     
  Significant variables N = 0
Clinical variable #34: 'LYMPH_NODES_EXAMINED_HE_COUNT'

No variable related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

Table S39.  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 #35: 'LYMPH_NODES_EXAMINED'

No variable related to 'LYMPH_NODES_EXAMINED'.

Table S40.  Basic characteristics of clinical feature: 'LYMPH_NODES_EXAMINED'

LYMPH_NODES_EXAMINED Mean (SD) 21.53 (13)
  Significant variables N = 0
Clinical variable #36: 'KERATINIZATION_SQUAMOUS_CELL'

One variable related to 'KERATINIZATION_SQUAMOUS_CELL'.

Table S41.  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 S42.  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 1283.5 0.0362 0.0724 0.6173
Clinical variable #37: 'INITIAL_PATHOLOGIC_DX_YEAR'

One variable related to 'INITIAL_PATHOLOGIC_DX_YEAR'.

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

INITIAL_PATHOLOGIC_DX_YEAR Mean (SD) 2007.67 (5.1)
  Significant variables N = 1
  pos. correlated 0
  neg. correlated 1
List of one variable associated with 'INITIAL_PATHOLOGIC_DX_YEAR'

Table S44.  Get Full Table List of one variable significantly correlated to 'INITIAL_PATHOLOGIC_DX_YEAR' by Spearman correlation test

SpearmanCorr corrP Q
MUTATIONRATE_SILENT -0.1527 0.03452 0.069
Clinical variable #38: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

No variable related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.

Table S45.  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 #39: 'HEIGHT_CM_AT_DIAGNOSIS'

No variable related to 'HEIGHT_CM_AT_DIAGNOSIS'.

Table S46.  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 #40: 'CORPUS_INVOLVEMENT'

No variable related to 'CORPUS_INVOLVEMENT'.

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

CORPUS_INVOLVEMENT Labels N
  ABSENT 88
  PRESENT 16
     
  Significant variables N = 0
Clinical variable #41: 'CHEMO_CONCURRENT_TYPE'

No variable related to 'CHEMO_CONCURRENT_TYPE'.

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

CHEMO_CONCURRENT_TYPE Labels N
  CARBOPLATIN 2
  CISPLATIN 16
  OTHER 1
     
  Significant variables N = 0
Clinical variable #42: 'CERVIX_SUV_RESULTS'

No variable related to 'CERVIX_SUV_RESULTS'.

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

CERVIX_SUV_RESULTS Mean (SD) 11.79 (3.8)
  Significant variables N = 0
Clinical variable #43: 'AJCC_TUMOR_PATHOLOGIC_PT'

No variable related to 'AJCC_TUMOR_PATHOLOGIC_PT'.

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

AJCC_TUMOR_PATHOLOGIC_PT Labels N
  T1A 1
  T1A1 1
  T1B 23
  T1B1 59
  T1B2 22
  T2 4
  T2A 7
  T2A1 6
  T2A2 10
  T2B 13
  T3 1
  T3B 2
  T4 2
  TX 9
     
  Significant variables N = 0
Clinical variable #44: 'AGE_AT_DIAGNOSIS'

2 variables related to 'AGE_AT_DIAGNOSIS'.

Table S51.  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 S52.  Get Full Table List of 2 variables significantly correlated to 'AGE_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
MUTATIONRATE_SILENT 0.338 1.43e-06 2.86e-06
MUTATIONRATE_NONSYNONYMOUS 0.3339 1.959e-06 2.86e-06
Clinical variable #45: 'STAGE_EVENT.CLINICAL_STAGE'

No variable related to 'STAGE_EVENT.CLINICAL_STAGE'.

Table S53.  Basic characteristics of clinical feature: 'STAGE_EVENT.CLINICAL_STAGE'

STAGE_EVENT.CLINICAL_STAGE Labels N
  STAGE I 4
  STAGE IA 2
  STAGE IA1 1
  STAGE IA2 1
  STAGE IB 28
  STAGE IB1 52
  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 = 45

Survival analysis

For survival clinical features, Wald's test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values using the 'coxph' function in R. Kaplan-Meier survival curves were plot using the four quartile subgroups of patients based on expression levels

Correlation analysis

For continuous numerical clinical features, Spearman's rank correlation coefficients (Spearman 1904) and two-tailed P values were estimated using 'cor.test' function in R

Student's t-test analysis

For two-class clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2-expression levels between the two clinical classes using 't.test' function in R

ANOVA analysis

For multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Andersen and Gill, Cox's regression model for counting processes, a large sample study, Annals of Statistics 10(4):1100-1120 (1982)
[2] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)
[3] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[4] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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