Correlation between miRseq expression and clinical features
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C10K27JR
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between miRseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C10K27JR
Overview
Introduction

This pipeline uses various statistical tests to identify miRs whose log2 expression levels correlated to selected clinical features.

Summary

Testing the association between 543 miRs and 45 clinical features across 304 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 26 clinical features related to at least one miRs.

  • 30 miRs correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • HSA-MIR-502 ,  HSA-MIR-150 ,  HSA-MIR-532 ,  HSA-MIR-361 ,  HSA-MIR-378C ,  ...

  • 30 miRs correlated to 'YEARS_TO_BIRTH'.

    • HSA-MIR-424 ,  HSA-MIR-455 ,  HSA-MIR-1468 ,  HSA-MIR-503 ,  HSA-MIR-450A-2 ,  ...

  • 30 miRs correlated to 'PATHOLOGY_T_STAGE'.

    • HSA-MIR-144 ,  HSA-MIR-486 ,  HSA-MIR-451 ,  HSA-MIR-424 ,  HSA-MIR-185 ,  ...

  • 30 miRs correlated to 'HISTOLOGICAL_TYPE'.

    • HSA-MIR-205 ,  HSA-MIR-375 ,  HSA-MIR-944 ,  HSA-MIR-194-2 ,  HSA-MIR-10A ,  ...

  • 30 miRs correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

    • HSA-MIR-19A ,  HSA-MIR-660 ,  HSA-MIR-212 ,  HSA-MIR-19B-2 ,  HSA-MIR-20A ,  ...

  • 6 miRs correlated to 'RACE'.

    • HSA-MIR-24-2 ,  HSA-MIR-185 ,  HSA-MIR-3130-1 ,  HSA-MIR-2355 ,  HSA-MIR-190 ,  ...

  • 10 miRs correlated to 'ETHNICITY'.

    • HSA-MIR-144 ,  HSA-MIR-486 ,  HSA-MIR-600 ,  HSA-MIR-451 ,  HSA-MIR-127 ,  ...

  • 30 miRs correlated to 'WEIGHT_KG_AT_DIAGNOSIS'.

    • HSA-MIR-592 ,  HSA-MIR-548B ,  HSA-MIR-181C ,  HSA-MIR-3690 ,  HSA-MIR-766 ,  ...

  • 30 miRs correlated to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.

    • HSA-MIR-185 ,  HSA-MIR-1274B ,  HSA-MIR-486 ,  HSA-MIR-19A ,  HSA-MIR-639 ,  ...

  • 30 miRs correlated to 'NEOPLASM_HISTOLOGIC_GRADE'.

    • HSA-MIR-486 ,  HSA-MIR-144 ,  HSA-MIR-421 ,  HSA-MIR-185 ,  HSA-MIR-23B ,  ...

  • 5 miRs correlated to 'TOBACCO_SMOKING_YEAR_STOPPED'.

    • HSA-MIR-18A ,  HSA-MIR-19A ,  HSA-MIR-598 ,  HSA-MIR-19B-2 ,  HSA-MIR-20A

  • 30 miRs correlated to 'TOBACCO_SMOKING_HISTORY'.

    • HSA-MIR-33A ,  HSA-MIR-146B ,  HSA-LET-7B ,  HSA-MIR-4326 ,  HSA-MIR-151 ,  ...

  • 30 miRs correlated to 'RADIATION_TOTAL_DOSE'.

    • HSA-MIR-215 ,  HSA-MIR-19A ,  HSA-MIR-3130-1 ,  HSA-MIR-19B-2 ,  HSA-MIR-326 ,  ...

  • 30 miRs correlated to 'RADIATION_THERAPY_TYPE'.

    • HSA-MIR-19A ,  HSA-MIR-212 ,  HSA-MIR-660 ,  HSA-MIR-1274B ,  HSA-MIR-19B-2 ,  ...

  • 30 miRs correlated to 'RADIATION_THERAPY_SITE'.

    • HSA-MIR-212 ,  HSA-MIR-3677 ,  HSA-MIR-1247 ,  HSA-MIR-323B ,  HSA-MIR-3136 ,  ...

  • 30 miRs correlated to 'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.

    • HSA-MIR-185 ,  HSA-MIR-340 ,  HSA-MIR-758 ,  HSA-MIR-146B ,  HSA-MIR-19A ,  ...

  • 4 miRs correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

    • HSA-MIR-1287 ,  HSA-MIR-19A ,  HSA-MIR-212 ,  HSA-MIR-151

  • 1 miR correlated to 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.

    • HSA-MIR-26B

  • 30 miRs correlated to 'MENOPAUSE_STATUS'.

    • HSA-MIR-424 ,  HSA-MIR-125B-2 ,  HSA-MIR-503 ,  HSA-MIR-1468 ,  HSA-LET-7C ,  ...

  • 1 miR correlated to 'LYMPHOVASCULAR_INVOLVEMENT'.

    • HSA-MIR-421

  • 25 miRs correlated to 'KERATINIZATION_SQUAMOUS_CELL'.

    • HSA-MIR-27A ,  HSA-MIR-152 ,  HSA-MIR-23C ,  HSA-MIR-23A ,  HSA-MIR-193A ,  ...

  • 30 miRs correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.

    • HSA-MIR-1274B ,  HSA-MIR-212 ,  HSA-MIR-19A ,  HSA-MIR-660 ,  HSA-MIR-326 ,  ...

  • 13 miRs correlated to 'HEIGHT_CM_AT_DIAGNOSIS'.

    • HSA-MIR-320B-2 ,  HSA-MIR-320E ,  HSA-MIR-320D-1 ,  HSA-MIR-320C-1 ,  HSA-MIR-548Q ,  ...

  • 12 miRs correlated to 'AJCC_TUMOR_PATHOLOGIC_PT'.

    • HSA-MIR-144 ,  HSA-MIR-486 ,  HSA-MIR-451 ,  HSA-MIR-218-2 ,  HSA-MIR-497 ,  ...

  • 30 miRs correlated to 'AGE_AT_DIAGNOSIS'.

    • HSA-MIR-424 ,  HSA-MIR-455 ,  HSA-MIR-1468 ,  HSA-MIR-503 ,  HSA-MIR-450A-2 ,  ...

  • 9 miRs correlated to 'STAGE_EVENT.CLINICAL_STAGE'.

    • HSA-MIR-144 ,  HSA-MIR-451 ,  HSA-MIR-486 ,  HSA-MIR-3610 ,  HSA-MIR-424 ,  ...

  • No miRs correlated to 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'NUMBER_PACK_YEARS_SMOKED', 'NUMBER_OF_LYMPH_NODES', 'TUMOR_STATUS', 'TOBACCO_SMOKING_PACK_YEARS_SMOKED', 'PATIENT.AGEBEGANSMOKINGINYEARS', 'RADIATION_THERAPY_STATUS', 'RADIATION_ADJUVANT_UNITS', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PREGNANCIES_COUNT_ECTOPIC', 'POS_LYMPH_NODE_LOCATION', 'LYMPH_NODES_EXAMINED_HE_COUNT', 'LYMPH_NODES_EXAMINED', 'HISTORY_HORMONAL_CONTRACEPTIVES_USE', '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 miRs that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.

Clinical feature Statistical test Significant miRs Associated with                 Associated with
DAYS_TO_DEATH_OR_LAST_FUP Cox regression test N=30 shorter survival N=3 longer survival N=27
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=11 lower stage N=19
PATHOLOGY_N_STAGE Wilcoxon test   N=0        
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
RADIATIONS_RADIATION_REGIMENINDICATION Wilcoxon test N=30 yes N=30 no N=0
NUMBER_PACK_YEARS_SMOKED Spearman correlation test   N=0        
NUMBER_OF_LYMPH_NODES Spearman correlation test   N=0        
RACE Kruskal-Wallis test N=6        
ETHNICITY Wilcoxon test N=10 not hispanic or latino N=10 hispanic or latino N=0
WEIGHT_KG_AT_DIAGNOSIS Spearman correlation test N=30 higher weight_kg_at_diagnosis N=27 lower weight_kg_at_diagnosis N=3
TUMOR_STATUS Wilcoxon test   N=0        
TUMOR_SAMPLE_PROCUREMENT_COUNTRY Kruskal-Wallis test N=30        
NEOPLASM_HISTOLOGIC_GRADE Kruskal-Wallis test N=30        
TOBACCO_SMOKING_YEAR_STOPPED Spearman correlation test N=5 higher tobacco_smoking_year_stopped N=4 lower tobacco_smoking_year_stopped N=1
TOBACCO_SMOKING_PACK_YEARS_SMOKED Spearman correlation test   N=0        
TOBACCO_SMOKING_HISTORY Kruskal-Wallis test N=30        
PATIENT AGEBEGANSMOKINGINYEARS Spearman correlation test   N=0        
RADIATION_TOTAL_DOSE Spearman correlation test N=30 higher radiation_total_dose N=23 lower radiation_total_dose N=7
RADIATION_THERAPY_TYPE Kruskal-Wallis test N=30        
RADIATION_THERAPY_STATUS Wilcoxon test   N=0        
RADIATION_THERAPY_SITE Kruskal-Wallis test N=30        
RADIATION_ADJUVANT_UNITS Wilcoxon test   N=0        
PREGNANCIES_COUNT_TOTAL Spearman correlation test   N=0        
PREGNANCIES_COUNT_STILLBIRTH Spearman correlation test   N=0        
PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT Spearman correlation test N=30 higher patient_patientpregnancyspontaneousabortioncount N=12 lower patient_patientpregnancyspontaneousabortioncount N=18
PREGNANCIES_COUNT_LIVE_BIRTH Spearman correlation test N=4 higher pregnancies_count_live_birth N=1 lower pregnancies_count_live_birth N=3
PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT Spearman correlation test N=1 higher patient_patientpregnancytherapeuticabortioncount N=0 lower patient_patientpregnancytherapeuticabortioncount N=1
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=1 present N=1 absent 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=25 non-keratinizing squamous cell carcinoma N=25 keratinizing squamous cell carcinoma N=0
INITIAL_PATHOLOGIC_DX_YEAR Spearman correlation test N=30 higher initial_pathologic_dx_year N=9 lower initial_pathologic_dx_year N=21
HISTORY_HORMONAL_CONTRACEPTIVES_USE Kruskal-Wallis test   N=0        
HEIGHT_CM_AT_DIAGNOSIS Spearman correlation test N=13 higher height_cm_at_diagnosis N=13 lower height_cm_at_diagnosis 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=12        
AGE_AT_DIAGNOSIS Spearman correlation test N=30 higher age_at_diagnosis N=14 lower age_at_diagnosis N=16
STAGE_EVENT CLINICAL_STAGE Kruskal-Wallis test N=9        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

30 miRs 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=20.1)
  censored N = 234
  death N = 69
     
  Significant markers N = 30
  associated with shorter survival 3
  associated with longer survival 27
List of top 10 miRs differentially expressed by 'DAYS_TO_DEATH_OR_LAST_FUP'

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

HazardRatio Wald_P Q C_index
HSA-MIR-502 0.53 7.212e-06 0.0022 0.337
HSA-MIR-150 0.72 8.165e-06 0.0022 0.337
HSA-MIR-532 0.48 3.138e-05 0.0057 0.362
HSA-MIR-361 0.51 5.718e-05 0.0078 0.369
HSA-MIR-378C 0.67 0.0001276 0.014 0.331
HSA-MIR-3607 0.67 0.0001967 0.018 0.395
HSA-MIR-142 0.69 0.0003263 0.025 0.358
HSA-MIR-101-1 0.59 0.0004055 0.028 0.346
HSA-MIR-188 0.65 0.000806 0.049 0.397
HSA-MIR-541 1.45 0.00127 0.069 0.668
Clinical variable #2: 'YEARS_TO_BIRTH'

30 miRs related to 'YEARS_TO_BIRTH'.

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

YEARS_TO_BIRTH Mean (SD) 48.11 (14)
  Significant markers N = 30
  pos. correlated 12
  neg. correlated 18
List of top 10 miRs differentially expressed by 'YEARS_TO_BIRTH'

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

SpearmanCorr corrP Q
HSA-MIR-424 -0.3031 8.569e-08 4.65e-05
HSA-MIR-455 -0.2858 4.78e-07 0.00013
HSA-MIR-1468 0.2657 3.564e-06 0.000645
HSA-MIR-503 -0.2298 5.893e-05 0.00742
HSA-MIR-450A-2 -0.2278 6.833e-05 0.00742
HSA-MIR-31 -0.2192 0.0001293 0.0117
HSA-MIR-204 0.2226 0.0001984 0.0154
HSA-MIR-653 0.2019 0.0004952 0.0336
HSA-MIR-133A-2 0.2683 0.0007381 0.0438
HSA-MIR-95 -0.1934 0.0008069 0.0438
Clinical variable #3: 'PATHOLOGY_T_STAGE'

30 miRs related to 'PATHOLOGY_T_STAGE'.

Table S5.  Basic characteristics of clinical feature: 'PATHOLOGY_T_STAGE'

PATHOLOGY_T_STAGE Mean (SD) 1.59 (0.82)
  N
  T1 140
  T2 70
  T3 21
  T4 10
     
  Significant markers N = 30
  pos. correlated 11
  neg. correlated 19
List of top 10 miRs differentially expressed by 'PATHOLOGY_T_STAGE'

Table S6.  Get Full Table List of top 10 miRs significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-144 0.3311 1.417e-07 7.69e-05
HSA-MIR-486 0.3159 5.509e-07 0.00015
HSA-MIR-451 0.3089 1.002e-06 0.00017
HSA-MIR-424 -0.3063 1.252e-06 0.00017
HSA-MIR-185 0.2883 5.393e-06 0.000586
HSA-MIR-450A-2 -0.2625 3.685e-05 0.00333
HSA-MIR-1247 -0.2487 9.86e-05 0.00718
HSA-MIR-181A-1 0.2471 0.0001058 0.00718
HSA-MIR-10A -0.241 0.000158 0.00951
HSA-MIR-103-1 0.2394 0.0001752 0.00951
Clinical variable #4: 'PATHOLOGY_N_STAGE'

No miR related to 'PATHOLOGY_N_STAGE'.

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

PATHOLOGY_N_STAGE Labels N
  N0 133
  N1 59
     
  Significant markers N = 0
Clinical variable #5: 'PATHOLOGY_M_STAGE'

No miR related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 115
  class1 10
     
  Significant markers N = 0
Clinical variable #6: 'HISTOLOGICAL_TYPE'

30 miRs related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  ADENOSQUAMOUS 5
  CERVICAL SQUAMOUS CELL CARCINOMA 253
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA 22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE 15
     
  Significant markers N = 30
List of top 10 miRs differentially expressed by 'HISTOLOGICAL_TYPE'

Table S10.  Get Full Table List of top 10 miRs differentially expressed by 'HISTOLOGICAL_TYPE'

kruskal_wallis_P Q
HSA-MIR-205 3.256e-21 1.77e-18
HSA-MIR-375 1.975e-18 5.36e-16
HSA-MIR-944 3.587e-18 6.49e-16
HSA-MIR-194-2 1.977e-14 2.68e-12
HSA-MIR-10A 1.901e-13 2.06e-11
HSA-MIR-194-1 2.364e-13 2.14e-11
HSA-MIR-192 2.941e-13 2.28e-11
HSA-MIR-1293 8.623e-13 5.85e-11
HSA-MIR-203 3.144e-12 1.9e-10
HSA-MIR-221 3.927e-11 2.13e-09
Clinical variable #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

30 miRs related to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

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

RADIATIONS_RADIATION_REGIMENINDICATION Labels N
  NO 35
  YES 269
     
  Significant markers N = 30
  Higher in YES 30
  Higher in NO 0
List of top 10 miRs differentially expressed by 'RADIATIONS_RADIATION_REGIMENINDICATION'

Table S12.  Get Full Table List of top 10 miRs differentially expressed by 'RADIATIONS_RADIATION_REGIMENINDICATION'

W(pos if higher in 'YES') wilcoxontestP Q AUC
HSA-MIR-19A 8197 9.868e-13 5.36e-10 0.8706
HSA-MIR-660 7947 3.561e-11 9.67e-09 0.8441
HSA-MIR-212 1511 6.431e-11 1.16e-08 0.8395
HSA-MIR-19B-2 7851 1.318e-10 1.79e-08 0.8339
HSA-MIR-20A 7783 3.257e-10 3.54e-08 0.8267
HSA-MIR-15A 7765 4.125e-10 3.73e-08 0.8247
HSA-MIR-338 7622 2.571e-09 1.99e-07 0.8096
HSA-MIR-143 1823 3.734e-09 2.53e-07 0.8064
HSA-MIR-1274B 1822 4.434e-09 2.68e-07 0.805
HSA-MIR-362 7432 2.57e-08 1.4e-06 0.7894
Clinical variable #8: 'NUMBER_PACK_YEARS_SMOKED'

No miR 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'

No miR related to 'NUMBER_OF_LYMPH_NODES'.

Table S14.  Basic characteristics of clinical feature: 'NUMBER_OF_LYMPH_NODES'

NUMBER_OF_LYMPH_NODES Mean (SD) 1.05 (2.4)
  Significant markers N = 0
Clinical variable #10: 'RACE'

6 miRs related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 8
  ASIAN 19
  BLACK OR AFRICAN AMERICAN 30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 2
  WHITE 210
     
  Significant markers N = 6
List of 6 miRs differentially expressed by 'RACE'

Table S16.  Get Full Table List of 6 miRs differentially expressed by 'RACE'

kruskal_wallis_P Q
HSA-MIR-24-2 0.0008379 0.177
HSA-MIR-185 0.00084 0.177
HSA-MIR-3130-1 0.001025 0.177
HSA-MIR-2355 0.001303 0.177
HSA-MIR-190 0.001661 0.18
HSA-MIR-454 0.002177 0.197
Clinical variable #11: 'ETHNICITY'

10 miRs related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 24
  NOT HISPANIC OR LATINO 169
     
  Significant markers N = 10
  Higher in NOT HISPANIC OR LATINO 10
  Higher in HISPANIC OR LATINO 0
Clinical variable #12: 'WEIGHT_KG_AT_DIAGNOSIS'

30 miRs related to 'WEIGHT_KG_AT_DIAGNOSIS'.

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

WEIGHT_KG_AT_DIAGNOSIS Mean (SD) 73.26 (21)
  Significant markers N = 30
  pos. correlated 27
  neg. correlated 3
List of top 10 miRs differentially expressed by 'WEIGHT_KG_AT_DIAGNOSIS'

Table S20.  Get Full Table List of top 10 miRs significantly correlated to 'WEIGHT_KG_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-592 0.2384 6.959e-05 0.0378
HSA-MIR-548B 0.2096 0.0009163 0.141
HSA-MIR-181C 0.1967 0.00102 0.141
HSA-MIR-3690 0.2077 0.001998 0.141
HSA-MIR-766 0.1848 0.002053 0.141
HSA-MIR-3130-1 0.1852 0.002167 0.141
HSA-MIR-639 0.205 0.002412 0.141
HSA-MIR-223 -0.1815 0.00247 0.141
HSA-MIR-518C 0.2761 0.002478 0.141
HSA-MIR-24-1 0.1795 0.002763 0.141
Clinical variable #13: 'TUMOR_STATUS'

No miR related to 'TUMOR_STATUS'.

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

TUMOR_STATUS Labels N
  TUMOR FREE 139
  WITH TUMOR 44
     
  Significant markers N = 0
Clinical variable #14: 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

30 miRs related to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.

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

TUMOR_SAMPLE_PROCUREMENT_COUNTRY Labels N
  BRAZIL 54
  CANADA 5
  NIGERIA 1
  RUSSIA 12
  UKRAINE 7
  UNITED STATES 211
  VIETNAM 14
     
  Significant markers N = 30
List of top 10 miRs differentially expressed by 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

Table S23.  Get Full Table List of top 10 miRs differentially expressed by 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

kruskal_wallis_P Q
HSA-MIR-185 5.825e-12 3.16e-09
HSA-MIR-1274B 4.861e-10 1.32e-07
HSA-MIR-486 8.999e-09 1.63e-06
HSA-MIR-19A 1.684e-08 1.75e-06
HSA-MIR-639 1.822e-08 1.75e-06
HSA-MIR-144 1.93e-08 1.75e-06
HSA-MIR-340 4.844e-07 3.76e-05
HSA-MIR-451 6.315e-07 3.86e-05
HSA-MIR-3130-1 6.397e-07 3.86e-05
HSA-MIR-3610 1.68e-06 8.21e-05
Clinical variable #15: 'NEOPLASM_HISTOLOGIC_GRADE'

30 miRs related to 'NEOPLASM_HISTOLOGIC_GRADE'.

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

NEOPLASM_HISTOLOGIC_GRADE Labels N
  G1 18
  G2 136
  G3 118
  G4 1
  GX 24
     
  Significant markers N = 30
List of top 10 miRs differentially expressed by 'NEOPLASM_HISTOLOGIC_GRADE'

Table S25.  Get Full Table List of top 10 miRs differentially expressed by 'NEOPLASM_HISTOLOGIC_GRADE'

kruskal_wallis_P Q
HSA-MIR-486 0.0002344 0.0551
HSA-MIR-144 0.0003582 0.0551
HSA-MIR-421 0.000398 0.0551
HSA-MIR-185 0.0004058 0.0551
HSA-MIR-23B 0.0006216 0.0675
HSA-MIR-19A 0.0009452 0.0794
HSA-MIR-496 0.001024 0.0794
HSA-MIR-346 0.001686 0.105
HSA-MIR-153-2 0.002053 0.105
HSA-MIR-17 0.002098 0.105
Clinical variable #16: 'TOBACCO_SMOKING_YEAR_STOPPED'

5 miRs related to 'TOBACCO_SMOKING_YEAR_STOPPED'.

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

TOBACCO_SMOKING_YEAR_STOPPED Mean (SD) 1999.69 (14)
  Significant markers N = 5
  pos. correlated 4
  neg. correlated 1
List of 5 miRs differentially expressed by 'TOBACCO_SMOKING_YEAR_STOPPED'

Table S27.  Get Full Table List of 5 miRs significantly correlated to 'TOBACCO_SMOKING_YEAR_STOPPED' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-18A 0.4792 0.001325 0.286
HSA-MIR-19A 0.4737 0.00153 0.286
HSA-MIR-598 -0.4721 0.001596 0.286
HSA-MIR-19B-2 0.4613 0.002106 0.286
HSA-MIR-20A 0.4517 0.002674 0.29
Clinical variable #17: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'

No miR related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.

Table S28.  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 #18: 'TOBACCO_SMOKING_HISTORY'

30 miRs related to 'TOBACCO_SMOKING_HISTORY'.

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

TOBACCO_SMOKING_HISTORY Labels N
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS 39
  CURRENT REFORMED SMOKER FOR > 15 YEARS 9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED 4
  CURRENT SMOKER 64
  LIFELONG NON-SMOKER 145
     
  Significant markers N = 30
List of top 10 miRs differentially expressed by 'TOBACCO_SMOKING_HISTORY'

Table S30.  Get Full Table List of top 10 miRs differentially expressed by 'TOBACCO_SMOKING_HISTORY'

kruskal_wallis_P Q
HSA-MIR-33A 0.0008336 0.206
HSA-MIR-146B 0.001828 0.206
HSA-LET-7B 0.002361 0.206
HSA-MIR-4326 0.002452 0.206
HSA-MIR-151 0.003171 0.206
HSA-MIR-27A 0.003426 0.206
HSA-MIR-128-2 0.003579 0.206
HSA-MIR-214 0.003629 0.206
HSA-MIR-1274B 0.003704 0.206
HSA-MIR-455 0.003913 0.206
Clinical variable #19: 'PATIENT.AGEBEGANSMOKINGINYEARS'

No miR related to 'PATIENT.AGEBEGANSMOKINGINYEARS'.

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

PATIENT.AGEBEGANSMOKINGINYEARS Mean (SD) 21.14 (7.7)
  Significant markers N = 0
Clinical variable #20: 'RADIATION_TOTAL_DOSE'

30 miRs related to 'RADIATION_TOTAL_DOSE'.

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

RADIATION_TOTAL_DOSE Mean (SD) 3635.38 (1700)
  Significant markers N = 30
  pos. correlated 23
  neg. correlated 7
List of top 10 miRs differentially expressed by 'RADIATION_TOTAL_DOSE'

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

SpearmanCorr corrP Q
HSA-MIR-215 0.3922 7.545e-07 0.00041
HSA-MIR-19A -0.3715 3.097e-06 0.000841
HSA-MIR-3130-1 0.3641 5.813e-06 0.00105
HSA-MIR-19B-2 -0.333 3.328e-05 0.00452
HSA-MIR-326 0.3163 8.983e-05 0.00976
HSA-MIR-1274B 0.3052 0.0001619 0.0146
HSA-LET-7A-2 0.291 0.000317 0.0188
HSA-LET-7A-3 0.29 0.000334 0.0188
HSA-MIR-20A -0.2899 0.0003356 0.0188
HSA-LET-7A-1 0.2893 0.0003457 0.0188
Clinical variable #21: 'RADIATION_THERAPY_TYPE'

30 miRs related to 'RADIATION_THERAPY_TYPE'.

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

RADIATION_THERAPY_TYPE Labels N
  COMBINATION 20
  EXTERNAL 104
  EXTERNAL BEAM 15
  IMPLANTS 1
  INTERNAL 25
     
  Significant markers N = 30
List of top 10 miRs differentially expressed by 'RADIATION_THERAPY_TYPE'

Table S35.  Get Full Table List of top 10 miRs differentially expressed by 'RADIATION_THERAPY_TYPE'

kruskal_wallis_P Q
HSA-MIR-19A 2.241e-12 1.22e-09
HSA-MIR-212 1.993e-11 5.41e-09
HSA-MIR-660 2.856e-10 5.17e-08
HSA-MIR-1274B 4.046e-10 5.49e-08
HSA-MIR-19B-2 7.024e-10 7.63e-08
HSA-MIR-326 8.481e-10 7.68e-08
HSA-MIR-20A 6.062e-09 4.7e-07
HSA-MIR-338 1.056e-08 6.73e-07
HSA-MIR-362 1.116e-08 6.73e-07
HSA-MIR-15A 1.373e-08 7.46e-07
Clinical variable #22: 'RADIATION_THERAPY_STATUS'

No miR related to 'RADIATION_THERAPY_STATUS'.

Table S36.  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 #23: 'RADIATION_THERAPY_SITE'

30 miRs related to 'RADIATION_THERAPY_SITE'.

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

RADIATION_THERAPY_SITE Labels N
  DISTANT RECURRENCE 2
  LOCAL RECURRENCE 2
  PRIMARY TUMOR FIELD 38
  REGIONAL SITE 33
     
  Significant markers N = 30
List of top 10 miRs differentially expressed by 'RADIATION_THERAPY_SITE'

Table S38.  Get Full Table List of top 10 miRs differentially expressed by 'RADIATION_THERAPY_SITE'

kruskal_wallis_P Q
HSA-MIR-212 0.0001522 0.0826
HSA-MIR-3677 0.0005539 0.15
HSA-MIR-1247 0.0008483 0.154
HSA-MIR-323B 0.001609 0.163
HSA-MIR-3136 0.001711 0.163
HSA-MIR-29A 0.002248 0.163
HSA-MIR-134 0.002318 0.163
HSA-MIR-377 0.002775 0.163
HSA-MIR-1287 0.002931 0.163
HSA-MIR-511-2 0.002993 0.163
Clinical variable #24: 'RADIATION_ADJUVANT_UNITS'

No miR related to 'RADIATION_ADJUVANT_UNITS'.

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

RADIATION_ADJUVANT_UNITS Labels N
  CGY 58
  GY 5
     
  Significant markers N = 0
Clinical variable #25: 'PREGNANCIES_COUNT_TOTAL'

No miR related to 'PREGNANCIES_COUNT_TOTAL'.

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

PREGNANCIES_COUNT_TOTAL Mean (SD) 3.62 (2.6)
  Significant markers N = 0
Clinical variable #26: 'PREGNANCIES_COUNT_STILLBIRTH'

No miR related to 'PREGNANCIES_COUNT_STILLBIRTH'.

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

PREGNANCIES_COUNT_STILLBIRTH Mean (SD) 0.07 (0.35)
  Value N
  0 105
  1 5
  3 1
     
  Significant markers N = 0
Clinical variable #27: 'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

30 miRs related to 'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.

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

PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT Mean (SD) 0.55 (0.95)
  Significant markers N = 30
  pos. correlated 12
  neg. correlated 18
List of top 10 miRs differentially expressed by 'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

Table S43.  Get Full Table List of top 10 miRs significantly correlated to 'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-185 0.3595 8.35e-06 0.00453
HSA-MIR-340 0.2933 0.0003273 0.0545
HSA-MIR-758 -0.2902 0.0003803 0.0545
HSA-MIR-146B 0.2891 0.0004012 0.0545
HSA-MIR-19A 0.2762 0.0007378 0.0601
HSA-MIR-216A -0.3797 0.0008482 0.0601
HSA-MIR-539 -0.269 0.001111 0.0601
HSA-MIR-379 -0.2659 0.001178 0.0601
HSA-LET-7G 0.2658 0.001185 0.0601
HSA-MIR-134 -0.2612 0.001452 0.0601
Clinical variable #28: 'PREGNANCIES_COUNT_LIVE_BIRTH'

4 miRs related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

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

PREGNANCIES_COUNT_LIVE_BIRTH Mean (SD) 2.85 (2.1)
  Significant markers N = 4
  pos. correlated 1
  neg. correlated 3
List of 4 miRs differentially expressed by 'PREGNANCIES_COUNT_LIVE_BIRTH'

Table S45.  Get Full Table List of 4 miRs significantly correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-1287 -0.2379 0.0001071 0.0582
HSA-MIR-19A 0.2045 0.0009117 0.248
HSA-MIR-212 -0.194 0.001677 0.253
HSA-MIR-151 -0.1921 0.001864 0.253
Clinical variable #29: 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

One miR related to 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.

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

PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT Mean (SD) 0.86 (1.8)
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one miR differentially expressed by 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

Table S47.  Get Full Table List of one miR significantly correlated to 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-26B -0.3184 0.0003715 0.202
Clinical variable #30: 'PREGNANCIES_COUNT_ECTOPIC'

No miR related to 'PREGNANCIES_COUNT_ECTOPIC'.

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

PREGNANCIES_COUNT_ECTOPIC Mean (SD) 0.11 (0.34)
  Value N
  0 103
  1 11
  2 1
     
  Significant markers N = 0
Clinical variable #31: 'POS_LYMPH_NODE_LOCATION'

No miR related to 'POS_LYMPH_NODE_LOCATION'.

Table S49.  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 39
  POSITIVE BLADDER MARGIN 1
  POSITIVE VAGINAL MARGIN 10
     
  Significant markers N = 0
Clinical variable #32: 'MENOPAUSE_STATUS'

30 miRs related to 'MENOPAUSE_STATUS'.

Table S50.  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) 83
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT) 124
     
  Significant markers N = 30
List of top 10 miRs differentially expressed by 'MENOPAUSE_STATUS'

Table S51.  Get Full Table List of top 10 miRs differentially expressed by 'MENOPAUSE_STATUS'

kruskal_wallis_P Q
HSA-MIR-424 4.12e-05 0.0137
HSA-MIR-125B-2 5.035e-05 0.0137
HSA-MIR-503 8.157e-05 0.0141
HSA-MIR-1468 0.0001224 0.0141
HSA-LET-7C 0.0001445 0.0141
HSA-MIR-99A 0.000156 0.0141
HSA-MIR-1274B 0.001043 0.0809
HSA-MIR-455 0.001741 0.118
HSA-MIR-4326 0.002326 0.125
HSA-MIR-338 0.002493 0.125
Clinical variable #33: 'LYMPHOVASCULAR_INVOLVEMENT'

One miR related to 'LYMPHOVASCULAR_INVOLVEMENT'.

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

LYMPHOVASCULAR_INVOLVEMENT Labels N
  ABSENT 71
  PRESENT 79
     
  Significant markers N = 1
  Higher in PRESENT 1
  Higher in ABSENT 0
List of one miR differentially expressed by 'LYMPHOVASCULAR_INVOLVEMENT'

Table S53.  Get Full Table List of one miR differentially expressed by 'LYMPHOVASCULAR_INVOLVEMENT'

W(pos if higher in 'PRESENT') wilcoxontestP Q AUC
HSA-MIR-421 c("3685", "0.0005022") c("3685", "0.0005022") 0.273 0.6654
Clinical variable #34: 'LYMPH_NODES_EXAMINED_HE_COUNT'

No miR related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

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

LYMPH_NODES_EXAMINED_HE_COUNT Mean (SD) 1.05 (2.4)
  Significant markers N = 0
Clinical variable #35: 'LYMPH_NODES_EXAMINED'

No miR related to 'LYMPH_NODES_EXAMINED'.

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

LYMPH_NODES_EXAMINED Mean (SD) 22.35 (13)
  Significant markers N = 0
Clinical variable #36: 'KERATINIZATION_SQUAMOUS_CELL'

25 miRs related to 'KERATINIZATION_SQUAMOUS_CELL'.

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

KERATINIZATION_SQUAMOUS_CELL Labels N
  KERATINIZING SQUAMOUS CELL CARCINOMA 54
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA 119
     
  Significant markers N = 25
  Higher in NON-KERATINIZING SQUAMOUS CELL CARCINOMA 25
  Higher in KERATINIZING SQUAMOUS CELL CARCINOMA 0
List of top 10 miRs differentially expressed by 'KERATINIZATION_SQUAMOUS_CELL'

Table S57.  Get Full Table List of top 10 miRs differentially expressed by 'KERATINIZATION_SQUAMOUS_CELL'

W(pos if higher in 'NON-KERATINIZING SQUAMOUS CELL CARCINOMA') wilcoxontestP Q AUC
HSA-MIR-27A 1997 6.834e-05 0.0291 0.6892
HSA-MIR-152 2030 0.0001071 0.0291 0.6841
HSA-MIR-23C 1512 0.0004324 0.0783 0.6809
HSA-MIR-23A 2201 0.0009207 0.116 0.6575
HSA-MIR-193A 2214 0.001071 0.116 0.6555
HSA-MIR-191 4154 0.002062 0.168 0.6464
HSA-MIR-30C-2 4140 0.002404 0.168 0.6443
HSA-MIR-944 2268 0.002469 0.168 0.6441
HSA-MIR-24-2 2307 0.003013 0.182 0.641
HSA-MIR-93 4092 0.004002 0.217 0.6368
Clinical variable #37: 'INITIAL_PATHOLOGIC_DX_YEAR'

30 miRs related to 'INITIAL_PATHOLOGIC_DX_YEAR'.

Table S58.  Basic characteristics of clinical feature: 'INITIAL_PATHOLOGIC_DX_YEAR'

INITIAL_PATHOLOGIC_DX_YEAR Mean (SD) 2008.29 (4.8)
  Significant markers N = 30
  pos. correlated 9
  neg. correlated 21
List of top 10 miRs differentially expressed by 'INITIAL_PATHOLOGIC_DX_YEAR'

Table S59.  Get Full Table List of top 10 miRs significantly correlated to 'INITIAL_PATHOLOGIC_DX_YEAR' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-1274B -0.4137 7.802e-14 4.24e-11
HSA-MIR-212 -0.3732 2.04e-11 5.54e-09
HSA-MIR-19A 0.3697 3.267e-11 5.91e-09
HSA-MIR-660 0.3647 6.199e-11 8.42e-09
HSA-MIR-326 -0.3485 6.174e-10 6.7e-08
HSA-MIR-24-2 -0.3417 1.076e-09 9.74e-08
HSA-MIR-15A 0.3328 3.057e-09 2.37e-07
HSA-MIR-143 -0.3291 4.655e-09 3.16e-07
HSA-MIR-19B-2 0.3247 7.647e-09 4.61e-07
HSA-MIR-3130-1 -0.3253 9.536e-09 5.18e-07
Clinical variable #38: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

No miR related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.

Table S60.  Basic characteristics of clinical feature: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

HISTORY_HORMONAL_CONTRACEPTIVES_USE Labels N
  CURRENT USER 15
  FORMER USER 53
  NEVER USED 89
     
  Significant markers N = 0
Clinical variable #39: 'HEIGHT_CM_AT_DIAGNOSIS'

13 miRs related to 'HEIGHT_CM_AT_DIAGNOSIS'.

Table S61.  Basic characteristics of clinical feature: 'HEIGHT_CM_AT_DIAGNOSIS'

HEIGHT_CM_AT_DIAGNOSIS Mean (SD) 161.02 (7.3)
  Significant markers N = 13
  pos. correlated 13
  neg. correlated 0
List of top 10 miRs differentially expressed by 'HEIGHT_CM_AT_DIAGNOSIS'

Table S62.  Get Full Table List of top 10 miRs significantly correlated to 'HEIGHT_CM_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-320B-2 0.2645 1.441e-05 0.00782
HSA-MIR-320E 0.3409 0.0002348 0.051
HSA-MIR-320D-1 0.2481 0.000282 0.051
HSA-MIR-320C-1 0.2189 0.0006215 0.0634
HSA-MIR-548Q 0.2505 0.0007697 0.0634
HSA-MIR-3130-1 0.2066 0.0008405 0.0634
HSA-MIR-551A 0.2477 0.0008874 0.0634
HSA-MIR-99B 0.2033 0.0009347 0.0634
HSA-MIR-1274B 0.1996 0.001212 0.0731
HSA-MIR-23C 0.214 0.001405 0.0763
Clinical variable #40: 'CORPUS_INVOLVEMENT'

No miR related to 'CORPUS_INVOLVEMENT'.

Table S63.  Basic characteristics of clinical feature: 'CORPUS_INVOLVEMENT'

CORPUS_INVOLVEMENT Labels N
  ABSENT 99
  PRESENT 18
     
  Significant markers N = 0
Clinical variable #41: 'CHEMO_CONCURRENT_TYPE'

No miR related to 'CHEMO_CONCURRENT_TYPE'.

Table S64.  Basic characteristics of clinical feature: 'CHEMO_CONCURRENT_TYPE'

CHEMO_CONCURRENT_TYPE Labels N
  CARBOPLATIN 3
  CISPLATIN 18
  OTHER 1
     
  Significant markers N = 0
Clinical variable #42: 'CERVIX_SUV_RESULTS'

No miR related to 'CERVIX_SUV_RESULTS'.

Table S65.  Basic characteristics of clinical feature: 'CERVIX_SUV_RESULTS'

CERVIX_SUV_RESULTS Mean (SD) 13.22 (7.2)
  Significant markers N = 0
Clinical variable #43: 'AJCC_TUMOR_PATHOLOGIC_PT'

12 miRs related to 'AJCC_TUMOR_PATHOLOGIC_PT'.

Table S66.  Basic characteristics of clinical feature: 'AJCC_TUMOR_PATHOLOGIC_PT'

AJCC_TUMOR_PATHOLOGIC_PT Labels N
  T1A1 1
  T1B 36
  T1B1 72
  T1B2 31
  T2 6
  T2A 10
  T2A1 7
  T2A2 10
  T2B 37
  T3 2
  T3A 2
  T3B 17
  T4 10
  TIS 1
  TX 17
     
  Significant markers N = 12
List of top 10 miRs differentially expressed by 'AJCC_TUMOR_PATHOLOGIC_PT'

Table S67.  Get Full Table List of top 10 miRs differentially expressed by 'AJCC_TUMOR_PATHOLOGIC_PT'

kruskal_wallis_P Q
HSA-MIR-144 2.848e-07 0.000155
HSA-MIR-486 1.203e-06 0.000327
HSA-MIR-451 2.069e-06 0.000375
HSA-MIR-218-2 0.0002529 0.0343
HSA-MIR-497 0.0004087 0.0435
HSA-MIR-185 0.0004802 0.0435
HSA-MIR-450A-2 0.001479 0.112
HSA-MIR-145 0.001651 0.112
HSA-MIR-101-1 0.002006 0.121
HSA-MIR-424 0.002226 0.121
Clinical variable #44: 'AGE_AT_DIAGNOSIS'

30 miRs related to 'AGE_AT_DIAGNOSIS'.

Table S68.  Basic characteristics of clinical feature: 'AGE_AT_DIAGNOSIS'

AGE_AT_DIAGNOSIS Mean (SD) 48.21 (14)
  Significant markers N = 30
  pos. correlated 14
  neg. correlated 16
List of top 10 miRs differentially expressed by 'AGE_AT_DIAGNOSIS'

Table S69.  Get Full Table List of top 10 miRs significantly correlated to 'AGE_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-424 -0.3073 4.554e-08 2.47e-05
HSA-MIR-455 -0.2791 7.646e-07 0.000208
HSA-MIR-1468 0.2644 3.434e-06 0.000622
HSA-MIR-503 -0.2343 3.704e-05 0.00503
HSA-MIR-450A-2 -0.2276 6.187e-05 0.00672
HSA-MIR-204 0.2285 0.0001176 0.0106
HSA-MIR-31 -0.2088 0.0002457 0.0191
HSA-MIR-653 0.2072 0.0003171 0.0215
HSA-MIR-133A-2 0.2693 0.0006492 0.0392
HSA-MIR-95 -0.188 0.00105 0.0548
Clinical variable #45: 'STAGE_EVENT.CLINICAL_STAGE'

9 miRs related to 'STAGE_EVENT.CLINICAL_STAGE'.

Table S70.  Basic characteristics of clinical feature: 'STAGE_EVENT.CLINICAL_STAGE'

STAGE_EVENT.CLINICAL_STAGE Labels N
  STAGE I 5
  STAGE IA 1
  STAGE IA1 1
  STAGE IA2 1
  STAGE IB 37
  STAGE IB1 78
  STAGE IB2 38
  STAGE II 5
  STAGE IIA 9
  STAGE IIA1 5
  STAGE IIA2 7
  STAGE IIB 43
  STAGE III 1
  STAGE IIIA 3
  STAGE IIIB 42
  STAGE IVA 9
  STAGE IVB 12
     
  Significant markers N = 9
List of 9 miRs differentially expressed by 'STAGE_EVENT.CLINICAL_STAGE'

Table S71.  Get Full Table List of 9 miRs differentially expressed by 'STAGE_EVENT.CLINICAL_STAGE'

kruskal_wallis_P Q
HSA-MIR-144 2.591e-05 0.00914
HSA-MIR-451 3.868e-05 0.00914
HSA-MIR-486 5.051e-05 0.00914
HSA-MIR-3610 0.0005171 0.0702
HSA-MIR-424 0.0006644 0.0722
HSA-MIR-185 0.001093 0.0902
HSA-MIR-218-2 0.001163 0.0902
HSA-MIR-140 0.002919 0.194
HSA-MIR-193A 0.003208 0.194
Methods & Data
Input

  • Expresson data file = CESC-TP.miRseq_RPKM_log2.txt

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

  • Number of patients = 304

  • Number of miRs = 543

  • Number of clinical features = 45

Selected clinical features

  • For clinical features selected for this analysis and their value conozzle.versions, please find a documentation on selected CDEs .

  • 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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