Correlation between mRNAseq expression and clinical features
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1XD10DB
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1XD10DB
Overview
Introduction

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

Summary

Testing the association between 18199 genes and 42 clinical features across 180 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 14 clinical features related to at least one genes.

  • 4 genes correlated to 'Time to Death'.

    • GATS|352954 ,  ZER1|10444 ,  FAM70B|348013 ,  UBAC1|10422

  • 14 genes correlated to 'AGE'.

    • NXNL2|158046 ,  LOC440356|440356 ,  RARB|5915 ,  INF2|64423 ,  C9ORF167|54863 ,  ...

  • 1 gene correlated to 'PATHOLOGY.N.STAGE'.

    • ART3|419

  • 1723 genes correlated to 'HISTOLOGICAL.TYPE'.

    • TP63|8626 ,  DNALI1|7802 ,  GPR109A|338442 ,  DEPDC6|64798 ,  PLCH1|23007 ,  ...

  • 1 gene correlated to 'NUMBER.OF.LYMPH.NODES'.

    • ART3|419

  • 1 gene correlated to 'RACE'.

    • XKR9|389668

  • 3 genes correlated to 'WEIGHT_KG_AT_DIAGNOSIS'.

    • HCG26|352961 ,  JMJD5|79831 ,  FAAH2|158584

  • 1 gene correlated to 'MENOPAUSE_STATUS'.

    • SSBP3|23648

  • 1 gene correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

    • ART3|419

  • 1 gene correlated to 'LYMPH_NODES_EXAMINED'.

    • MAGEA10|4109

  • 1 gene correlated to 'KERATINIZATION_SQUAMOUS_CELL'.

    • QKI|9444

  • 2 genes correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.

    • C9ORF171|389799 ,  SNAPC5|10302

  • 1 gene correlated to 'CERVIX_SUV_RESULTS'.

    • TEX14|56155

  • 15 genes correlated to 'AGE_AT_DIAGNOSIS'.

    • NXNL2|158046 ,  LOC440356|440356 ,  C9ORF167|54863 ,  GPR97|222487 ,  IGSF9|57549 ,  ...

  • No genes correlated to 'PATHOLOGY.T.STAGE', 'PATHOLOGY.M.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'NUMBERPACKYEARSSMOKED', 'ETHNICITY', 'TUMOR_STATUS', 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY', 'NEOPLASMHISTOLOGICGRADE', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_PACK_YEARS_SMOKED', 'TOBACCO_SMOKING_HISTORY', 'PATIENT.AGEBEGANSMOKINGINYEARS', 'RADIATION_THERAPY_TYPE', 'RADIATION_ADJUVANT_UNITS', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT', 'PREGNANCIES_COUNT_LIVE_BIRTH', 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT', 'PREGNANCIES_COUNT_ECTOPIC', 'LYMPH_NODE_LOCATION', 'LOCATION_OF_POSITIVE_MARGINS', 'LYMPHOVASCULAR_INVOLVEMENT', 'HYSTERECTOMY_TYPE', 'HISTORY_HORMONAL_CONTRACEPTIVES_USE', 'HEIGHT_CM_AT_DIAGNOSIS', 'CORPUS_INVOLVEMENT', and 'AJCC_TUMOR_PATHOLOGIC_PT'.

Results
Overview of the results

Complete statistical result table is provided in Supplement Table 1

Table 1.  Get Full Table This table shows the clinical features, statistical methods used, and the number of genes that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.

Clinical feature Statistical test Significant genes Associated with                 Associated with
Time to Death Cox regression test N=4 shorter survival N=1 longer survival N=3
AGE Spearman correlation test N=14 older N=7 younger N=7
PATHOLOGY T STAGE Spearman correlation test   N=0        
PATHOLOGY N STAGE Wilcoxon test N=1 class1 N=1 class0 N=0
PATHOLOGY M STAGE Kruskal-Wallis test   N=0        
HISTOLOGICAL TYPE Kruskal-Wallis test N=1723        
RADIATIONS RADIATION REGIMENINDICATION Wilcoxon test   N=0        
NUMBERPACKYEARSSMOKED Spearman correlation test   N=0        
NUMBER OF LYMPH NODES Spearman correlation test N=1 higher number.of.lymph.nodes N=0 lower number.of.lymph.nodes N=1
RACE Kruskal-Wallis test N=1        
ETHNICITY Wilcoxon test   N=0        
WEIGHT_KG_AT_DIAGNOSIS Spearman correlation test N=3 higher weight_kg_at_diagnosis N=3 lower weight_kg_at_diagnosis 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=0        
TOBACCO_SMOKING_HISTORY Kruskal-Wallis test   N=0        
PATIENT AGEBEGANSMOKINGINYEARS Spearman correlation test   N=0        
RADIATION_THERAPY_TYPE 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=0        
PATIENT PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT Spearman correlation test   N=0        
PREGNANCIES_COUNT_ECTOPIC Spearman correlation test   N=0        
LYMPH_NODE_LOCATION Kruskal-Wallis test   N=0        
LOCATION_OF_POSITIVE_MARGINS Kruskal-Wallis test   N=0        
MENOPAUSE_STATUS Kruskal-Wallis test N=1        
LYMPHOVASCULAR_INVOLVEMENT Wilcoxon test   N=0        
LYMPH_NODES_EXAMINED_HE_COUNT Spearman correlation test N=1 higher lymph_nodes_examined_he_count N=0 lower lymph_nodes_examined_he_count N=1
LYMPH_NODES_EXAMINED Spearman correlation test N=1 higher lymph_nodes_examined N=0 lower lymph_nodes_examined N=1
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=2 higher initial_pathologic_dx_year N=1 lower initial_pathologic_dx_year N=1
HYSTERECTOMY_TYPE Kruskal-Wallis test   N=0        
HISTORY_HORMONAL_CONTRACEPTIVES_USE Kruskal-Wallis test   N=0        
HEIGHT_CM_AT_DIAGNOSIS Spearman correlation test   N=0        
CORPUS_INVOLVEMENT Wilcoxon test   N=0        
CERVIX_SUV_RESULTS Spearman correlation test N=1 higher cervix_suv_results N=0 lower cervix_suv_results N=1
AJCC_TUMOR_PATHOLOGIC_PT Kruskal-Wallis test   N=0        
AGE_AT_DIAGNOSIS Spearman correlation test N=15 higher age_at_diagnosis N=8 lower age_at_diagnosis N=7
Clinical variable #1: 'Time to Death'

4 genes related to 'Time to Death'.

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

Time to Death Duration (Months) 0-182.9 (median=13.6)
  censored N = 140
  death N = 33
     
  Significant markers N = 4
  associated with shorter survival 1
  associated with longer survival 3
List of 4 genes differentially expressed by 'Time to Death'

Table S2.  Get Full Table List of 4 genes significantly associated with 'Time to Death' by Cox regression test

HazardRatio Wald_P Q C_index
GATS|352954 0.49 3.159e-07 0.0057 0.24
ZER1|10444 0.13 9.559e-07 0.017 0.273
FAM70B|348013 1.98 4.591e-06 0.084 0.72
UBAC1|10422 0.17 1.087e-05 0.2 0.28
Clinical variable #2: 'AGE'

14 genes related to 'AGE'.

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

AGE Mean (SD) 47.44 (13)
  Significant markers N = 14
  pos. correlated 7
  neg. correlated 7
List of top 10 genes differentially expressed by 'AGE'

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

SpearmanCorr corrP Q
NXNL2|158046 -0.4475 1.502e-09 2.73e-05
LOC440356|440356 0.369 1.577e-06 0.0287
RARB|5915 0.3483 1.767e-06 0.0322
INF2|64423 -0.3477 1.849e-06 0.0336
C9ORF167|54863 -0.3454 2.181e-06 0.0397
GPR97|222487 -0.3398 3.269e-06 0.0595
UNC119|9094 0.3371 3.944e-06 0.0717
IGSF9|57549 0.3343 4.797e-06 0.0873
PGR|5241 -0.3305 6.229e-06 0.113
RRAGD|58528 0.3265 8.191e-06 0.149
Clinical variable #3: 'PATHOLOGY.T.STAGE'

No gene related to 'PATHOLOGY.T.STAGE'.

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

PATHOLOGY.T.STAGE Mean (SD) 1.31 (0.54)
  N
  1 100
  2 37
  3 2
  4 1
     
  Significant markers N = 0
Clinical variable #4: 'PATHOLOGY.N.STAGE'

One gene related to 'PATHOLOGY.N.STAGE'.

Table S6.  Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'

PATHOLOGY.N.STAGE Labels N
  class0 89
  class1 42
     
  Significant markers N = 1
  Higher in class1 1
  Higher in class0 0
List of one gene differentially expressed by 'PATHOLOGY.N.STAGE'

Table S7.  Get Full Table List of one gene differentially expressed by 'PATHOLOGY.N.STAGE'

W(pos if higher in 'class1') wilcoxontestP Q AUC
ART3|419 677 8.549e-06 0.156 0.7612
Clinical variable #5: 'PATHOLOGY.M.STAGE'

No gene related to 'PATHOLOGY.M.STAGE'.

Table S8.  Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE Labels N
  M0 76
  M1 3
  MX 65
     
  Significant markers N = 0
Clinical variable #6: 'HISTOLOGICAL.TYPE'

1723 genes related to 'HISTOLOGICAL.TYPE'.

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

HISTOLOGICAL.TYPE Labels N
  ADENOSQUAMOUS 2
  CERVICAL SQUAMOUS CELL CARCINOMA 148
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA 20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE 4
     
  Significant markers N = 1723
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S10.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
TP63|8626 1.795e-14 3.27e-10
DNALI1|7802 3.577e-14 6.51e-10
GPR109A|338442 4.05e-14 7.37e-10
DEPDC6|64798 4.085e-14 7.43e-10
PLCH1|23007 5.288e-14 9.62e-10
BICD2|23299 5.591e-14 1.02e-09
GOLM1|51280 7.837e-14 1.43e-09
CABLES1|91768 9.298e-14 1.69e-09
SLC6A20|54716 1.092e-13 1.99e-09
PKP1|5317 1.244e-13 2.26e-09
Clinical variable #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

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

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 30
  YES 150
     
  Significant markers N = 0
Clinical variable #8: 'NUMBERPACKYEARSSMOKED'

No gene related to 'NUMBERPACKYEARSSMOKED'.

Table S12.  Basic characteristics of clinical feature: 'NUMBERPACKYEARSSMOKED'

NUMBERPACKYEARSSMOKED Mean (SD) 18.59 (12)
  Significant markers N = 0
Clinical variable #9: 'NUMBER.OF.LYMPH.NODES'

One gene related to 'NUMBER.OF.LYMPH.NODES'.

Table S13.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 1.07 (2.6)
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one gene differentially expressed by 'NUMBER.OF.LYMPH.NODES'

Table S14.  Get Full Table List of one gene significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
ART3|419 -0.4404 5.081e-06 0.0925
Clinical variable #10: 'RACE'

One gene related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 6
  ASIAN 15
  BLACK OR AFRICAN AMERICAN 18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 1
  WHITE 135
     
  Significant markers N = 1
List of one gene differentially expressed by 'RACE'

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

ANOVA_P Q
XKR9|389668 4.026e-06 0.0733
Clinical variable #11: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 12
  NOT HISPANIC OR LATINO 129
     
  Significant markers N = 0
Clinical variable #12: 'WEIGHT_KG_AT_DIAGNOSIS'

3 genes related to 'WEIGHT_KG_AT_DIAGNOSIS'.

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

WEIGHT_KG_AT_DIAGNOSIS Mean (SD) 75.31 (21)
  Significant markers N = 3
  pos. correlated 3
  neg. correlated 0
List of 3 genes differentially expressed by 'WEIGHT_KG_AT_DIAGNOSIS'

Table S19.  Get Full Table List of 3 genes significantly correlated to 'WEIGHT_KG_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
HCG26|352961 0.3621 1.631e-06 0.0297
JMJD5|79831 0.3366 9.217e-06 0.168
FAAH2|158584 0.331 1.328e-05 0.242
Clinical variable #13: 'TUMOR_STATUS'

No gene related to 'TUMOR_STATUS'.

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

TUMOR_STATUS Labels N
  TUMOR FREE 50
  WITH TUMOR 20
     
  Significant markers N = 0
Clinical variable #14: 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

No gene related to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.

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

TUMOR_SAMPLE_PROCUREMENT_COUNTRY Labels N
  NIGERIA 1
  RUSSIA 11
  UKRAINE 6
  UNITED STATES 150
  VIETNAM 12
     
  Significant markers N = 0
Clinical variable #15: 'NEOPLASMHISTOLOGICGRADE'

No gene related to 'NEOPLASMHISTOLOGICGRADE'.

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

NEOPLASMHISTOLOGICGRADE Labels N
  G1 14
  G2 85
  G3 74
  G4 1
  GX 5
     
  Significant markers N = 0
Clinical variable #16: 'TOBACCO_SMOKING_YEAR_STOPPED'

No gene related to 'TOBACCO_SMOKING_YEAR_STOPPED'.

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

TOBACCO_SMOKING_YEAR_STOPPED Mean (SD) 1997.72 (12)
  Significant markers N = 0
Clinical variable #17: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'

No gene related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.

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

TOBACCO_SMOKING_PACK_YEARS_SMOKED Mean (SD) 18.59 (12)
  Significant markers N = 0
Clinical variable #18: 'TOBACCO_SMOKING_HISTORY'

No gene related to 'TOBACCO_SMOKING_HISTORY'.

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

TOBACCO_SMOKING_HISTORY Labels N
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS 23
  CURRENT REFORMED SMOKER FOR > 15 YEARS 8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED 1
  CURRENT SMOKER 36
  LIFELONG NON-SMOKER 83
     
  Significant markers N = 0
Clinical variable #19: 'PATIENT.AGEBEGANSMOKINGINYEARS'

No gene related to 'PATIENT.AGEBEGANSMOKINGINYEARS'.

Table S26.  Basic characteristics of clinical feature: 'PATIENT.AGEBEGANSMOKINGINYEARS'

PATIENT.AGEBEGANSMOKINGINYEARS Mean (SD) 20.52 (6.3)
  Significant markers N = 0
Clinical variable #20: 'RADIATION_THERAPY_TYPE'

No gene related to 'RADIATION_THERAPY_TYPE'.

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

RADIATION_THERAPY_TYPE Labels N
  COMBINATION 17
  EXTERNAL 37
  EXTERNAL BEAM 14
  INTERNAL 5
     
  Significant markers N = 0
Clinical variable #21: 'RADIATION_ADJUVANT_UNITS'

No gene related to 'RADIATION_ADJUVANT_UNITS'.

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

RADIATION_ADJUVANT_UNITS Labels N
  CGY 12
  GY 3
     
  Significant markers N = 0
Clinical variable #22: 'PREGNANCIES_COUNT_TOTAL'

No gene related to 'PREGNANCIES_COUNT_TOTAL'.

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

PREGNANCIES_COUNT_TOTAL Mean (SD) 3.46 (2.5)
  Significant markers N = 0
Clinical variable #23: 'PREGNANCIES_COUNT_STILLBIRTH'

No gene 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 90
  1 5
  3 1
     
  Significant markers N = 0
Clinical variable #24: 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

No gene related to 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.

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

PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT Mean (SD) 0.31 (0.56)
  Value N
  0 78
  1 27
  2 2
  3 1
     
  Significant markers N = 0
Clinical variable #25: 'PREGNANCIES_COUNT_LIVE_BIRTH'

No gene related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

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

PREGNANCIES_COUNT_LIVE_BIRTH Mean (SD) 2.39 (1.7)
  Significant markers N = 0
Clinical variable #26: 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

No gene related to 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.

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

PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT Mean (SD) 0.92 (1.9)
  Significant markers N = 0
Clinical variable #27: 'PREGNANCIES_COUNT_ECTOPIC'

No gene related to 'PREGNANCIES_COUNT_ECTOPIC'.

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

PREGNANCIES_COUNT_ECTOPIC Mean (SD) 0.1 (0.34)
  Value N
  0 88
  1 8
  2 1
     
  Significant markers N = 0
Clinical variable #28: 'LYMPH_NODE_LOCATION'

No gene related to 'LYMPH_NODE_LOCATION'.

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

LYMPH_NODE_LOCATION Labels N
  2003 1
  2010 1
  COMMON ILIAC 1
  PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR) 39
     
  Significant markers N = 0
Clinical variable #29: 'LOCATION_OF_POSITIVE_MARGINS'

No gene related to 'LOCATION_OF_POSITIVE_MARGINS'.

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

LOCATION_OF_POSITIVE_MARGINS Labels N
  MACROSCOPIC PARAMETRIAL INVOLVEMENT 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT 6
  OTHER LOCATION, SPECIFY 12
  POSITIVE BLADDER MARGIN 1
  POSITIVE VAGINAL MARGIN 5
     
  Significant markers N = 0
Clinical variable #30: 'MENOPAUSE_STATUS'

One gene related to 'MENOPAUSE_STATUS'.

Table S37.  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) 53
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT) 81
     
  Significant markers N = 1
List of one gene differentially expressed by 'MENOPAUSE_STATUS'

Table S38.  Get Full Table List of one gene differentially expressed by 'MENOPAUSE_STATUS'

ANOVA_P Q
SSBP3|23648 2.204e-06 0.0401
Clinical variable #31: 'LYMPHOVASCULAR_INVOLVEMENT'

No gene related to 'LYMPHOVASCULAR_INVOLVEMENT'.

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

LYMPHOVASCULAR_INVOLVEMENT Labels N
  ABSENT 54
  PRESENT 62
     
  Significant markers N = 0
Clinical variable #32: 'LYMPH_NODES_EXAMINED_HE_COUNT'

One gene related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

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

LYMPH_NODES_EXAMINED_HE_COUNT Mean (SD) 1.07 (2.6)
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one gene differentially expressed by 'LYMPH_NODES_EXAMINED_HE_COUNT'

Table S41.  Get Full Table List of one gene significantly correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT' by Spearman correlation test

SpearmanCorr corrP Q
ART3|419 -0.4404 5.081e-06 0.0925
Clinical variable #33: 'LYMPH_NODES_EXAMINED'

One gene related to 'LYMPH_NODES_EXAMINED'.

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

LYMPH_NODES_EXAMINED Mean (SD) 22.28 (13)
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one gene differentially expressed by 'LYMPH_NODES_EXAMINED'

Table S43.  Get Full Table List of one gene significantly correlated to 'LYMPH_NODES_EXAMINED' by Spearman correlation test

SpearmanCorr corrP Q
MAGEA10|4109 -0.5824 1.621e-06 0.0295
Clinical variable #34: 'KERATINIZATION_SQUAMOUS_CELL'

One gene related to 'KERATINIZATION_SQUAMOUS_CELL'.

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

KERATINIZATION_SQUAMOUS_CELL Labels N
  KERATINIZING SQUAMOUS CELL CARCINOMA 39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA 81
     
  Significant markers N = 1
  Higher in NON-KERATINIZING SQUAMOUS CELL CARCINOMA 1
  Higher in KERATINIZING SQUAMOUS CELL CARCINOMA 0
List of one gene differentially expressed by 'KERATINIZATION_SQUAMOUS_CELL'

Table S45.  Get Full Table List of one gene differentially expressed by 'KERATINIZATION_SQUAMOUS_CELL'

W(pos if higher in 'NON-KERATINIZING SQUAMOUS CELL CARCINOMA') wilcoxontestP Q AUC
QKI|9444 792 1.036e-05 0.188 0.7493
Clinical variable #35: 'INITIAL_PATHOLOGIC_DX_YEAR'

2 genes related to 'INITIAL_PATHOLOGIC_DX_YEAR'.

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

INITIAL_PATHOLOGIC_DX_YEAR Mean (SD) 2007.5 (5.1)
  Significant markers N = 2
  pos. correlated 1
  neg. correlated 1
List of 2 genes differentially expressed by 'INITIAL_PATHOLOGIC_DX_YEAR'

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

SpearmanCorr corrP Q
C9ORF171|389799 0.4376 1.034e-05 0.188
SNAPC5|10302 -0.3158 1.576e-05 0.287
Clinical variable #36: 'HYSTERECTOMY_TYPE'

No gene related to 'HYSTERECTOMY_TYPE'.

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

HYSTERECTOMY_TYPE Labels N
  OTHER 3
  RADICAL HYSTERECTOMY 117
  SIMPLE HYSTERECTOMY 5
     
  Significant markers N = 0
Clinical variable #37: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

No gene related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.

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

HISTORY_HORMONAL_CONTRACEPTIVES_USE Labels N
  CURRENT USER 8
  FORMER USER 40
  NEVER USED 43
     
  Significant markers N = 0
Clinical variable #38: 'HEIGHT_CM_AT_DIAGNOSIS'

No gene related to 'HEIGHT_CM_AT_DIAGNOSIS'.

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

HEIGHT_CM_AT_DIAGNOSIS Mean (SD) 162.05 (6.9)
  Significant markers N = 0
Clinical variable #39: 'CORPUS_INVOLVEMENT'

No gene related to 'CORPUS_INVOLVEMENT'.

Table S51.  Basic characteristics of clinical feature: 'CORPUS_INVOLVEMENT'

CORPUS_INVOLVEMENT Labels N
  ABSENT 78
  PRESENT 14
     
  Significant markers N = 0
Clinical variable #40: 'CERVIX_SUV_RESULTS'

One gene related to 'CERVIX_SUV_RESULTS'.

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

CERVIX_SUV_RESULTS Mean (SD) 11.37 (4.1)
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one gene differentially expressed by 'CERVIX_SUV_RESULTS'

Table S53.  Get Full Table List of one gene significantly correlated to 'CERVIX_SUV_RESULTS' by Spearman correlation test

SpearmanCorr corrP Q
TEX14|56155 -1 5.511e-06 0.099
Clinical variable #41: 'AJCC_TUMOR_PATHOLOGIC_PT'

No gene related to 'AJCC_TUMOR_PATHOLOGIC_PT'.

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

AJCC_TUMOR_PATHOLOGIC_PT Labels N
  T1A 2
  T1A1 1
  T1B 23
  T1B1 52
  T1B2 22
  T2 3
  T2A 6
  T2A1 6
  T2A2 9
  T2B 13
  T3B 2
  T4 1
  TX 7
     
  Significant markers N = 0
Clinical variable #42: 'AGE_AT_DIAGNOSIS'

15 genes related to 'AGE_AT_DIAGNOSIS'.

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

AGE_AT_DIAGNOSIS Mean (SD) 47.52 (13)
  Significant markers N = 15
  pos. correlated 8
  neg. correlated 7
List of top 10 genes differentially expressed by 'AGE_AT_DIAGNOSIS'

Table S56.  Get Full Table List of top 10 genes significantly correlated to 'AGE_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
NXNL2|158046 -0.4475 1.502e-09 2.73e-05
LOC440356|440356 0.3769 8.324e-07 0.0151
C9ORF167|54863 -0.3487 1.615e-06 0.0294
GPR97|222487 -0.3467 1.863e-06 0.0339
IGSF9|57549 0.3398 3.053e-06 0.0555
UNC119|9094 0.3391 3.225e-06 0.0587
PGR|5241 -0.337 3.742e-06 0.0681
RARB|5915 0.3367 3.798e-06 0.0691
INF2|64423 -0.3336 4.732e-06 0.0861
RRAGD|58528 0.3293 6.365e-06 0.116
Methods & Data
Input

  • Expresson data file = CESC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

  • Number of patients = 180

  • Number of genes = 18199

  • Number of clinical features = 42

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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