Correlation between miRseq expression 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/C1C24V75
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between miRseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1C24V75
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 250 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 19 clinical features related to at least one miRs.

  • 9 miRs correlated to 'Time to Death'.

    • HSA-MIR-502 ,  HSA-MIR-532 ,  HSA-MIR-361 ,  HSA-MIR-150 ,  HSA-MIR-101-1 ,  ...

  • 8 miRs correlated to 'AGE'.

    • HSA-MIR-424 ,  HSA-MIR-1-2 ,  HSA-MIR-455 ,  HSA-MIR-503 ,  HSA-MIR-1468 ,  ...

  • 1 miR correlated to 'PATHOLOGY.T.STAGE'.

    • HSA-MIR-3150B

  • 40 miRs correlated to 'HISTOLOGICAL.TYPE'.

    • HSA-MIR-205 ,  HSA-MIR-375 ,  HSA-MIR-944 ,  HSA-MIR-194-2 ,  HSA-MIR-194-1 ,  ...

  • 47 miRs correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

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

  • 1 miR correlated to 'RACE'.

    • HSA-MIR-3130-1

  • 1 miR correlated to 'WEIGHT_KG_AT_DIAGNOSIS'.

    • HSA-MIR-592

  • 22 miRs correlated to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.

    • HSA-MIR-144 ,  HSA-MIR-1274B ,  HSA-MIR-486 ,  HSA-MIR-19A ,  HSA-MIR-451 ,  ...

  • 2 miRs correlated to 'RADIATION_TOTAL_DOSE'.

    • HSA-MIR-215 ,  HSA-MIR-194-1

  • 41 miRs correlated to 'RADIATION_THERAPY_TYPE'.

    • HSA-MIR-19A ,  HSA-MIR-212 ,  HSA-MIR-1274B ,  HSA-MIR-326 ,  HSA-MIR-19B-2 ,  ...

  • 1 miR correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

    • HSA-MIR-1287

  • 1 miR correlated to 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.

    • HSA-MIR-26B

  • 6 miRs correlated to 'MENOPAUSE_STATUS'.

    • HSA-MIR-125B-2 ,  HSA-LET-7C ,  HSA-MIR-99A ,  HSA-MIR-424 ,  HSA-MIR-503 ,  ...

  • 1 miR correlated to 'LYMPHOVASCULAR_INVOLVEMENT'.

    • HSA-MIR-421

  • 3 miRs correlated to 'KERATINIZATION_SQUAMOUS_CELL'.

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

  • 47 miRs correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.

    • HSA-MIR-212 ,  HSA-MIR-1274B ,  HSA-MIR-24-2 ,  HSA-MIR-326 ,  HSA-MIR-660 ,  ...

  • 2 miRs correlated to 'HEIGHT_CM_AT_DIAGNOSIS'.

    • HSA-MIR-320E ,  HSA-MIR-320B-2

  • 3 miRs correlated to 'AJCC_TUMOR_PATHOLOGIC_PT'.

    • HSA-MIR-144 ,  HSA-MIR-451 ,  HSA-MIR-486

  • 8 miRs correlated to 'AGE_AT_DIAGNOSIS'.

    • HSA-MIR-424 ,  HSA-MIR-1-2 ,  HSA-MIR-503 ,  HSA-MIR-455 ,  HSA-MIR-204 ,  ...

  • No miRs correlated to 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'NUMBERPACKYEARSSMOKED', 'NUMBER.OF.LYMPH.NODES', 'ETHNICITY', 'TUMOR_STATUS', 'NEOPLASMHISTOLOGICGRADE', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_PACK_YEARS_SMOKED', 'TOBACCO_SMOKING_HISTORY', 'PATIENT.AGEBEGANSMOKINGINYEARS', 'RADIATION_THERAPY_STATUS', 'RADIATION_THERAPY_SITE', 'RADIATION_ADJUVANT_UNITS', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT', 'PREGNANCIES_COUNT_ECTOPIC', 'POS_LYMPH_NODE_LOCATION', 'LYMPH_NODES_EXAMINED_HE_COUNT', 'LYMPH_NODES_EXAMINED', 'HISTORY_HORMONAL_CONTRACEPTIVES_USE', 'CORPUS_INVOLVEMENT', 'CHEMO_CONCURRENT_TYPE', 'CERVIX_SUV_RESULTS', 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 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
Time to Death Cox regression test N=9 shorter survival N=0 longer survival N=9
AGE Spearman correlation test N=8 older N=3 younger N=5
PATHOLOGY T STAGE Spearman correlation test N=1 higher stage N=0 lower stage N=1
PATHOLOGY N STAGE Wilcoxon test   N=0        
PATHOLOGY M STAGE Kruskal-Wallis test   N=0        
HISTOLOGICAL TYPE Kruskal-Wallis test N=40        
RADIATIONS RADIATION REGIMENINDICATION Wilcoxon test N=47 yes N=47 no N=0
NUMBERPACKYEARSSMOKED Spearman correlation test   N=0        
NUMBER OF LYMPH NODES Spearman correlation test   N=0        
RACE Kruskal-Wallis test N=1        
ETHNICITY Wilcoxon test   N=0        
WEIGHT_KG_AT_DIAGNOSIS Spearman correlation test N=1 higher weight_kg_at_diagnosis N=1 lower weight_kg_at_diagnosis N=0
TUMOR_STATUS Wilcoxon test   N=0        
TUMOR_SAMPLE_PROCUREMENT_COUNTRY Kruskal-Wallis test N=22        
NEOPLASMHISTOLOGICGRADE Kruskal-Wallis test   N=0        
TOBACCO_SMOKING_YEAR_STOPPED Spearman correlation test   N=0        
TOBACCO_SMOKING_PACK_YEARS_SMOKED Spearman correlation test   N=0        
TOBACCO_SMOKING_HISTORY Kruskal-Wallis test   N=0        
PATIENT AGEBEGANSMOKINGINYEARS Spearman correlation test   N=0        
RADIATION_TOTAL_DOSE Spearman correlation test N=2 higher radiation_total_dose N=2 lower radiation_total_dose N=0
RADIATION_THERAPY_TYPE Kruskal-Wallis test N=41        
RADIATION_THERAPY_STATUS Wilcoxon test   N=0        
RADIATION_THERAPY_SITE Kruskal-Wallis test   N=0        
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=0        
PREGNANCIES_COUNT_LIVE_BIRTH Spearman correlation test N=1 higher pregnancies_count_live_birth N=0 lower pregnancies_count_live_birth N=1
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=6        
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=3 non-keratinizing squamous cell carcinoma N=3 keratinizing squamous cell carcinoma N=0
INITIAL_PATHOLOGIC_DX_YEAR Spearman correlation test N=47 higher initial_pathologic_dx_year N=14 lower initial_pathologic_dx_year N=33
HISTORY_HORMONAL_CONTRACEPTIVES_USE Kruskal-Wallis test   N=0        
HEIGHT_CM_AT_DIAGNOSIS Spearman correlation test N=2 higher height_cm_at_diagnosis N=2 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=3        
AGE_AT_DIAGNOSIS Spearman correlation test N=8 higher age_at_diagnosis N=3 lower age_at_diagnosis N=5
STAGE_EVENT CLINICAL_STAGE Kruskal-Wallis test   N=0        
Clinical variable #1: 'Time to Death'

9 miRs related to 'Time to Death'.

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

Time to Death Duration (Months) 0-195.8 (median=16.1)
  censored N = 191
  death N = 54
     
  Significant markers N = 9
  associated with shorter survival 0
  associated with longer survival 9
List of 9 miRs differentially expressed by 'Time to Death'

Table S2.  Get Full Table List of 9 miRs significantly associated with 'Time to Death' by Cox regression test

HazardRatio Wald_P Q C_index
HSA-MIR-502 0.51 1.021e-05 0.0055 0.312
HSA-MIR-532 0.41 1.275e-05 0.0069 0.329
HSA-MIR-361 0.49 2.462e-05 0.013 0.356
HSA-MIR-150 0.73 7.38e-05 0.04 0.335
HSA-MIR-101-1 0.55 0.000131 0.071 0.322
HSA-MIR-378C 0.63 0.0001622 0.087 0.328
HSA-MIR-3607 0.66 0.0003218 0.17 0.376
HSA-MIR-142 0.67 0.0003792 0.2 0.352
HSA-MIR-188 0.59 0.0004311 0.23 0.37
Clinical variable #2: 'AGE'

8 miRs related to 'AGE'.

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

AGE Mean (SD) 47.58 (14)
  Significant markers N = 8
  pos. correlated 3
  neg. correlated 5
List of 8 miRs differentially expressed by 'AGE'

Table S4.  Get Full Table List of 8 miRs significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-424 -0.3018 1.416e-06 0.000769
HSA-MIR-1-2 0.2822 7.263e-06 0.00394
HSA-MIR-455 -0.2668 2.227e-05 0.012
HSA-MIR-503 -0.2539 5.629e-05 0.0304
HSA-MIR-1468 0.2533 6.078e-05 0.0328
HSA-MIR-204 0.2543 0.000103 0.0554
HSA-MIR-625 -0.2294 0.0002851 0.153
HSA-MIR-95 -0.2294 0.0003025 0.162
Clinical variable #3: 'PATHOLOGY.T.STAGE'

One miR related to 'PATHOLOGY.T.STAGE'.

Table S5.  Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE Mean (SD) 1.43 (0.68)
  N
  1 127
  2 52
  3 9
  4 4
     
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one miR differentially expressed by 'PATHOLOGY.T.STAGE'

Table S6.  Get Full Table List of one miR significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-3150B -0.2633 0.0005435 0.295
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
  class0 117
  class1 51
     
  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
  M0 99
  M1 8
  MX 96
     
  Significant markers N = 0
Clinical variable #6: 'HISTOLOGICAL.TYPE'

40 miRs related to 'HISTOLOGICAL.TYPE'.

Table S9.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  ADENOSQUAMOUS 5
  CERVICAL SQUAMOUS CELL CARCINOMA 209
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA 22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE 6
     
  Significant markers N = 40
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'

ANOVA_P Q
HSA-MIR-205 1.82e-16 9.88e-14
HSA-MIR-375 5.195e-15 2.82e-12
HSA-MIR-944 1.404e-13 7.6e-11
HSA-MIR-194-2 2.332e-11 1.26e-08
HSA-MIR-194-1 1.488e-10 8.02e-08
HSA-MIR-1293 2.494e-10 1.34e-07
HSA-MIR-192 2.951e-10 1.58e-07
HSA-MIR-10A 6.757e-10 3.62e-07
HSA-MIR-203 1.501e-09 8.03e-07
HSA-MIR-221 1.024e-08 5.47e-06
Clinical variable #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'

47 miRs related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S11.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 35
  YES 215
     
  Significant markers N = 47
  Higher in YES 47
  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 6358 6.115e-11 3.31e-08 0.8449
HSA-MIR-660 6297 1.69e-10 9.14e-08 0.8368
HSA-MIR-212 1354 1.283e-09 6.93e-07 0.8201
HSA-MIR-19B-2 6147 1.866e-09 1.01e-06 0.8169
HSA-MIR-20A 6143 1.986e-09 1.07e-06 0.8163
HSA-MIR-15A 6093 4.281e-09 2.3e-06 0.8097
HSA-MIR-362 5979 2.329e-08 1.25e-05 0.7946
HSA-MIR-143 1567 3.154e-08 1.69e-05 0.7918
HSA-MIR-338 5957 3.2e-08 1.71e-05 0.7916
HSA-MIR-93 5879 9.631e-08 5.13e-05 0.7813
Clinical variable #8: 'NUMBERPACKYEARSSMOKED'

No miR related to 'NUMBERPACKYEARSSMOKED'.

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

NUMBERPACKYEARSSMOKED Mean (SD) 18.81 (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) 1.08 (2.5)
  Significant markers N = 0
Clinical variable #10: 'RACE'

One miR 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 26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 1
  WHITE 178
     
  Significant markers N = 1
List of one miR differentially expressed by 'RACE'

Table S16.  Get Full Table List of one miR differentially expressed by 'RACE'

ANOVA_P Q
HSA-MIR-3130-1 0.0002724 0.148
Clinical variable #11: 'ETHNICITY'

No miR related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 17
  NOT HISPANIC OR LATINO 157
     
  Significant markers N = 0
Clinical variable #12: 'WEIGHT_KG_AT_DIAGNOSIS'

One miR related to 'WEIGHT_KG_AT_DIAGNOSIS'.

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

WEIGHT_KG_AT_DIAGNOSIS Mean (SD) 74.79 (22)
  Significant markers N = 1
  pos. correlated 1
  neg. correlated 0
List of one miR differentially expressed by 'WEIGHT_KG_AT_DIAGNOSIS'

Table S19.  Get Full Table List of one miR significantly correlated to 'WEIGHT_KG_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-592 0.2458 0.0001904 0.103
Clinical variable #13: 'TUMOR_STATUS'

No miR related to 'TUMOR_STATUS'.

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

TUMOR_STATUS Labels N
  TUMOR FREE 75
  WITH TUMOR 28
     
  Significant markers N = 0
Clinical variable #14: 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

22 miRs related to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.

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

TUMOR_SAMPLE_PROCUREMENT_COUNTRY Labels N
  BRAZIL 24
  CANADA 5
  NIGERIA 1
  RUSSIA 11
  UKRAINE 7
  UNITED STATES 188
  VIETNAM 14
     
  Significant markers N = 22
List of top 10 miRs differentially expressed by 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

Table S22.  Get Full Table List of top 10 miRs differentially expressed by 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

ANOVA_P Q
HSA-MIR-144 7.472e-08 4.06e-05
HSA-MIR-1274B 2.28e-07 0.000124
HSA-MIR-486 5.501e-07 0.000298
HSA-MIR-19A 2.093e-06 0.00113
HSA-MIR-451 5.276e-06 0.00284
HSA-MIR-340 6.085e-06 0.00327
HSA-MIR-185 9.451e-06 0.00508
HSA-MIR-3130-1 1.283e-05 0.00688
HSA-MIR-326 2.133e-05 0.0114
HSA-MIR-639 2.46e-05 0.0131
Clinical variable #15: 'NEOPLASMHISTOLOGICGRADE'

No miR related to 'NEOPLASMHISTOLOGICGRADE'.

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

NEOPLASMHISTOLOGICGRADE Labels N
  G1 17
  G2 113
  G3 102
  G4 1
  GX 14
     
  Significant markers N = 0
Clinical variable #16: 'TOBACCO_SMOKING_YEAR_STOPPED'

No miR related to 'TOBACCO_SMOKING_YEAR_STOPPED'.

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

TOBACCO_SMOKING_YEAR_STOPPED Mean (SD) 2000.41 (11)
  Significant markers N = 0
Clinical variable #17: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'

No miR 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) 18.81 (14)
  Significant markers N = 0
Clinical variable #18: 'TOBACCO_SMOKING_HISTORY'

No miR related to 'TOBACCO_SMOKING_HISTORY'.

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

TOBACCO_SMOKING_HISTORY Labels N
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS 33
  CURRENT REFORMED SMOKER FOR > 15 YEARS 8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED 3
  CURRENT SMOKER 54
  LIFELONG NON-SMOKER 114
     
  Significant markers N = 0
Clinical variable #19: 'PATIENT.AGEBEGANSMOKINGINYEARS'

No miR related to 'PATIENT.AGEBEGANSMOKINGINYEARS'.

Table S27.  Basic characteristics of clinical feature: 'PATIENT.AGEBEGANSMOKINGINYEARS'

PATIENT.AGEBEGANSMOKINGINYEARS Mean (SD) 21.43 (7.8)
  Significant markers N = 0
Clinical variable #20: 'RADIATION_TOTAL_DOSE'

2 miRs related to 'RADIATION_TOTAL_DOSE'.

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

RADIATION_TOTAL_DOSE Mean (SD) 3890.86 (1600)
  Significant markers N = 2
  pos. correlated 2
  neg. correlated 0
List of 2 miRs differentially expressed by 'RADIATION_TOTAL_DOSE'

Table S29.  Get Full Table List of 2 miRs significantly correlated to 'RADIATION_TOTAL_DOSE' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-215 0.3933 2.137e-05 0.0116
HSA-MIR-194-1 0.3268 0.000494 0.268
Clinical variable #21: 'RADIATION_THERAPY_TYPE'

41 miRs related to 'RADIATION_THERAPY_TYPE'.

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

RADIATION_THERAPY_TYPE Labels N
  COMBINATION 20
  EXTERNAL 77
  EXTERNAL BEAM 15
  IMPLANTS 1
  INTERNAL 12
     
  Significant markers N = 41
List of top 10 miRs differentially expressed by 'RADIATION_THERAPY_TYPE'

Table S31.  Get Full Table List of top 10 miRs differentially expressed by 'RADIATION_THERAPY_TYPE'

ANOVA_P Q
HSA-MIR-19A 4.455e-10 2.42e-07
HSA-MIR-212 7.233e-10 3.92e-07
HSA-MIR-1274B 1.49e-08 8.06e-06
HSA-MIR-326 1.862e-08 1.01e-05
HSA-MIR-19B-2 2.073e-08 1.12e-05
HSA-MIR-20A 5.684e-08 3.06e-05
HSA-MIR-660 6.72e-08 3.61e-05
HSA-MIR-143 1.51e-07 8.09e-05
HSA-MIR-15A 2.595e-07 0.000139
HSA-MIR-20B 5.818e-07 0.000311
Clinical variable #22: 'RADIATION_THERAPY_STATUS'

No miR related to 'RADIATION_THERAPY_STATUS'.

Table S32.  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'

No miR related to 'RADIATION_THERAPY_SITE'.

Table S33.  Basic characteristics of clinical feature: 'RADIATION_THERAPY_SITE'

RADIATION_THERAPY_SITE Labels N
  DISTANT RECURRENCE 2
  LOCAL RECURRENCE 2
  PRIMARY TUMOR FIELD 30
  REGIONAL SITE 16
     
  Significant markers N = 0
Clinical variable #24: 'RADIATION_ADJUVANT_UNITS'

No miR related to 'RADIATION_ADJUVANT_UNITS'.

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

RADIATION_ADJUVANT_UNITS Labels N
  CGY 36
  GY 3
     
  Significant markers N = 0
Clinical variable #25: 'PREGNANCIES_COUNT_TOTAL'

No miR related to 'PREGNANCIES_COUNT_TOTAL'.

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

PREGNANCIES_COUNT_TOTAL Mean (SD) 3.57 (2.5)
  Significant markers N = 0
Clinical variable #26: 'PREGNANCIES_COUNT_STILLBIRTH'

No miR related to 'PREGNANCIES_COUNT_STILLBIRTH'.

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

PREGNANCIES_COUNT_STILLBIRTH Mean (SD) 0.07 (0.35)
  Value N
  0 103
  1 5
  3 1
     
  Significant markers N = 0
Clinical variable #27: 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

No miR related to 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.

Table S37.  Basic characteristics of clinical feature: 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT Mean (SD) 0.46 (0.83)
  Significant markers N = 0
Clinical variable #28: 'PREGNANCIES_COUNT_LIVE_BIRTH'

One miR related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

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

PREGNANCIES_COUNT_LIVE_BIRTH Mean (SD) 2.65 (1.9)
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one miR differentially expressed by 'PREGNANCIES_COUNT_LIVE_BIRTH'

Table S39.  Get Full Table List of one miR significantly correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-1287 -0.235 0.0004399 0.239
Clinical variable #29: 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

One miR related to 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.

Table S40.  Basic characteristics of clinical feature: 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT Mean (SD) 0.87 (1.8)
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one miR differentially expressed by 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

Table S41.  Get Full Table List of one miR significantly correlated to 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-26B -0.3256 0.0003018 0.164
Clinical variable #30: 'PREGNANCIES_COUNT_ECTOPIC'

No miR related to 'PREGNANCIES_COUNT_ECTOPIC'.

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

PREGNANCIES_COUNT_ECTOPIC Mean (SD) 0.1 (0.33)
  Value N
  0 101
  1 9
  2 1
     
  Significant markers N = 0
Clinical variable #31: 'POS_LYMPH_NODE_LOCATION'

No miR related to 'POS_LYMPH_NODE_LOCATION'.

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

POS_LYMPH_NODE_LOCATION Labels N
  MACROSCOPIC PARAMETRIAL INVOLVEMENT 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT 7
  OTHER LOCATION, SPECIFY 33
  POSITIVE BLADDER MARGIN 1
  POSITIVE VAGINAL MARGIN 9
     
  Significant markers N = 0
Clinical variable #32: 'MENOPAUSE_STATUS'

6 miRs related to 'MENOPAUSE_STATUS'.

Table S44.  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) 16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY) 70
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT) 109
     
  Significant markers N = 6
List of 6 miRs differentially expressed by 'MENOPAUSE_STATUS'

Table S45.  Get Full Table List of 6 miRs differentially expressed by 'MENOPAUSE_STATUS'

ANOVA_P Q
HSA-MIR-125B-2 8.349e-06 0.00453
HSA-LET-7C 1.46e-05 0.00791
HSA-MIR-99A 1.881e-05 0.0102
HSA-MIR-424 0.0001242 0.0671
HSA-MIR-503 0.0001574 0.0849
HSA-MIR-4326 0.0004771 0.257
Clinical variable #33: 'LYMPHOVASCULAR_INVOLVEMENT'

One miR related to 'LYMPHOVASCULAR_INVOLVEMENT'.

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

LYMPHOVASCULAR_INVOLVEMENT Labels N
  ABSENT 69
  PRESENT 76
     
  Significant markers N = 1
  Higher in PRESENT 1
  Higher in ABSENT 0
List of one miR differentially expressed by 'LYMPHOVASCULAR_INVOLVEMENT'

Table S47.  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("3474", "0.0003954") c("3474", "0.0003954") 0.215 0.6713
Clinical variable #34: 'LYMPH_NODES_EXAMINED_HE_COUNT'

No miR related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

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

LYMPH_NODES_EXAMINED_HE_COUNT Mean (SD) 1.08 (2.5)
  Significant markers N = 0
Clinical variable #35: 'LYMPH_NODES_EXAMINED'

No miR related to 'LYMPH_NODES_EXAMINED'.

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

LYMPH_NODES_EXAMINED Mean (SD) 21.73 (12)
  Significant markers N = 0
Clinical variable #36: 'KERATINIZATION_SQUAMOUS_CELL'

3 miRs related to 'KERATINIZATION_SQUAMOUS_CELL'.

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

KERATINIZATION_SQUAMOUS_CELL Labels N
  KERATINIZING SQUAMOUS CELL CARCINOMA 49
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA 97
     
  Significant markers N = 3
  Higher in NON-KERATINIZING SQUAMOUS CELL CARCINOMA 3
  Higher in KERATINIZING SQUAMOUS CELL CARCINOMA 0
List of 3 miRs differentially expressed by 'KERATINIZATION_SQUAMOUS_CELL'

Table S51.  Get Full Table List of 3 miRs differentially expressed by 'KERATINIZATION_SQUAMOUS_CELL'

W(pos if higher in 'NON-KERATINIZING SQUAMOUS CELL CARCINOMA') wilcoxontestP Q AUC
HSA-MIR-27A 1472 0.0001794 0.0974 0.6903
HSA-MIR-152 1479 0.0002013 0.109 0.6888
HSA-MIR-23C 1091 0.0005009 0.271 0.6908
Clinical variable #37: 'INITIAL_PATHOLOGIC_DX_YEAR'

47 miRs related to 'INITIAL_PATHOLOGIC_DX_YEAR'.

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

INITIAL_PATHOLOGIC_DX_YEAR Mean (SD) 2007.73 (5)
  Significant markers N = 47
  pos. correlated 14
  neg. correlated 33
List of top 10 miRs differentially expressed by 'INITIAL_PATHOLOGIC_DX_YEAR'

Table S53.  Get Full Table List of top 10 miRs significantly correlated to 'INITIAL_PATHOLOGIC_DX_YEAR' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-212 -0.3826 4.571e-10 2.48e-07
HSA-MIR-1274B -0.3734 1.485e-09 8.05e-07
HSA-MIR-24-2 -0.3594 5.664e-09 3.06e-06
HSA-MIR-326 -0.361 5.936e-09 3.21e-06
HSA-MIR-660 0.3545 9.394e-09 5.06e-06
HSA-MIR-19A 0.3433 2.871e-08 1.54e-05
HSA-MIR-143 -0.3343 6.896e-08 3.7e-05
HSA-MIR-15A 0.3234 1.913e-07 0.000103
HSA-MIR-29A -0.3231 1.964e-07 0.000105
HSA-MIR-93 0.3197 2.677e-07 0.000143
Clinical variable #38: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

No miR related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.

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

HISTORY_HORMONAL_CONTRACEPTIVES_USE Labels N
  CURRENT USER 10
  FORMER USER 49
  NEVER USED 62
     
  Significant markers N = 0
Clinical variable #39: 'HEIGHT_CM_AT_DIAGNOSIS'

2 miRs related to 'HEIGHT_CM_AT_DIAGNOSIS'.

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

HEIGHT_CM_AT_DIAGNOSIS Mean (SD) 161.59 (7.1)
  Significant markers N = 2
  pos. correlated 2
  neg. correlated 0
List of 2 miRs differentially expressed by 'HEIGHT_CM_AT_DIAGNOSIS'

Table S56.  Get Full Table List of 2 miRs significantly correlated to 'HEIGHT_CM_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-320E 0.3609 0.0001442 0.0783
HSA-MIR-320B-2 0.2448 0.0002628 0.142
Clinical variable #40: 'CORPUS_INVOLVEMENT'

No miR related to 'CORPUS_INVOLVEMENT'.

Table S57.  Basic characteristics of clinical feature: 'CORPUS_INVOLVEMENT'

CORPUS_INVOLVEMENT Labels N
  ABSENT 96
  PRESENT 17
     
  Significant markers N = 0
Clinical variable #41: 'CHEMO_CONCURRENT_TYPE'

No miR related to 'CHEMO_CONCURRENT_TYPE'.

Table S58.  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 S59.  Basic characteristics of clinical feature: 'CERVIX_SUV_RESULTS'

CERVIX_SUV_RESULTS Mean (SD) 12.43 (5.5)
  Significant markers N = 0
Clinical variable #43: 'AJCC_TUMOR_PATHOLOGIC_PT'

3 miRs related to 'AJCC_TUMOR_PATHOLOGIC_PT'.

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

AJCC_TUMOR_PATHOLOGIC_PT Labels N
  T1A 1
  T1A1 1
  T1B 32
  T1B1 68
  T1B2 25
  T2 4
  T2A 8
  T2A1 7
  T2A2 10
  T2B 23
  T3 1
  T3B 8
  T4 4
  TIS 1
  TX 15
     
  Significant markers N = 3
List of 3 miRs differentially expressed by 'AJCC_TUMOR_PATHOLOGIC_PT'

Table S61.  Get Full Table List of 3 miRs differentially expressed by 'AJCC_TUMOR_PATHOLOGIC_PT'

ANOVA_P Q
HSA-MIR-144 3.948e-05 0.0214
HSA-MIR-451 5.694e-05 0.0309
HSA-MIR-486 0.0002794 0.151
Clinical variable #44: 'AGE_AT_DIAGNOSIS'

8 miRs related to 'AGE_AT_DIAGNOSIS'.

Table S62.  Basic characteristics of clinical feature: 'AGE_AT_DIAGNOSIS'

AGE_AT_DIAGNOSIS Mean (SD) 47.7 (13)
  Significant markers N = 8
  pos. correlated 3
  neg. correlated 5
List of 8 miRs differentially expressed by 'AGE_AT_DIAGNOSIS'

Table S63.  Get Full Table List of 8 miRs significantly correlated to 'AGE_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-424 -0.3083 6.657e-07 0.000361
HSA-MIR-1-2 0.2801 7.197e-06 0.0039
HSA-MIR-503 -0.2592 3.348e-05 0.0181
HSA-MIR-455 -0.2591 3.367e-05 0.0182
HSA-MIR-204 0.261 5.727e-05 0.0309
HSA-MIR-1468 0.2516 5.93e-05 0.0319
HSA-MIR-625 -0.2323 0.0002104 0.113
HSA-MIR-95 -0.222 0.0004276 0.229
Clinical variable #45: 'STAGE_EVENT.CLINICAL_STAGE'

No miR related to 'STAGE_EVENT.CLINICAL_STAGE'.

Table S64.  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 35
  STAGE IB1 70
  STAGE IB2 34
  STAGE II 4
  STAGE IIA 7
  STAGE IIA1 5
  STAGE IIA2 7
  STAGE IIB 27
  STAGE III 1
  STAGE IIIB 34
  STAGE IVA 5
  STAGE IVB 7
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 250

  • Number of miRs = 543

  • 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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