Correlation between RPPA 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/C1833R18
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between RPPA expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1833R18
Overview
Introduction

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

Summary

Testing the association between 192 genes and 44 clinical features across 172 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 16 clinical features related to at least one genes.

  • 10 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • EIF4EBP1|4E-BP1_PT70-R-V ,  CCND1|CYCLIN_D1-R-V ,  RAD51|RAD51-R-V ,  PECAM1|CD31-M-V ,  RAB11A RAB11B|RAB11-R-E ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • TGM2|TRANSGLUTAMINASE-M-V ,  BIRC2 |CIAP-R-V ,  YAP1|YAP-R-E ,  ESR1|ER-ALPHA-R-V ,  RAB11A RAB11B|RAB11-R-E ,  ...

  • 8 genes correlated to 'PATHOLOGY_T_STAGE'.

    • ANXA7 |ANNEXIN_VII-M-V ,  DVL3|DVL3-R-V ,  ERBB2|HER2_PY1248-R-C ,  PECAM1|CD31-M-V ,  SYK|SYK-M-V ,  ...

  • 15 genes correlated to 'HISTOLOGICAL_TYPE'.

    • NDRG1|NDRG1_PT346-R-V ,  EGFR|EGFR-R-V ,  C12ORF5|TIGAR-R-V ,  XRCC1|XRCC1-R-E ,  PRKAA1|AMPK_ALPHA-R-C ,  ...

  • 30 genes correlated to 'NUMBER_PACK_YEARS_SMOKED'.

    • MET|C-MET_PY1235-R-V ,  ARHI|ARHI-M-E ,  MAPK8|JNK_PT183_PY185-R-V ,  GSK3A GSK3B|GSK3-ALPHA-BETA-M-V ,  INPP4B|INPP4B-R-V ,  ...

  • 1 gene correlated to 'TUMOR_STATUS'.

    • SCD1|SCD1-M-V

  • 30 genes correlated to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.

    • MET|C-MET_PY1235-R-V ,  ARHI|ARHI-M-E ,  MAPK8|JNK_PT183_PY185-R-V ,  GSK3A GSK3B|GSK3-ALPHA-BETA-M-V ,  INPP4B|INPP4B-R-V ,  ...

  • 30 genes correlated to 'RADIATION_ADJUVANT_UNITS'.

    • BCL2L1|BCL-XL-R-V ,  MAPK9|JNK2-R-C ,  YWHAB|14-3-3_BETA-R-V ,  BRAF|B-RAF-M-C ,  STAT5A|STAT5-ALPHA-R-V ,  ...

  • 9 genes correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

    • ETS1|ETS-1-R-V ,  PKC|PKC-PAN_BETAII_PS660-R-V ,  DVL3|DVL3-R-V ,  SYK|SYK-M-V ,  BRCA2|BRCA2-R-C ,  ...

  • 7 genes correlated to 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.

    • RPS6KA1|P90RSK-R-C ,  EGFR|EGFR_PY1173-R-V ,  G6PD|G6PD-M-V ,  ARHI|ARHI-M-E ,  MYC|C-MYC-R-C ,  ...

  • 6 genes correlated to 'MENOPAUSE_STATUS'.

    • GAPDH|GAPDH-M-C ,  TGM2|TRANSGLUTAMINASE-M-V ,  BIRC2 |CIAP-R-V ,  CCNE1|CYCLIN_E1-M-V ,  STAT5A|STAT5-ALPHA-R-V ,  ...

  • 20 genes correlated to 'LYMPH_NODES_EXAMINED'.

    • PCNA|PCNA-M-C ,  YAP1|YAP_PS127-R-E ,  RICTOR|RICTOR-R-C ,  CDH3|P-CADHERIN-R-C ,  MYH11|MYH11-R-V ,  ...

  • 3 genes correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.

    • ASNS|ASNS-R-V ,  TP53|P53-R-E ,  ARHI|ARHI-M-E

  • 1 gene correlated to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.

    • PTEN|PTEN-R-V

  • 27 genes correlated to 'CERVIX_SUV_RESULTS'.

    • RPS6KA1|P90RSK_PT359_S363-R-C ,  RPS6|S6_PS235_S236-R-V ,  PARK7|DJ-1-R-E ,  CDKN1B|P27-R-V ,  YBX1|YB-1_PS102-R-V ,  ...

  • 30 genes correlated to 'AGE_AT_DIAGNOSIS'.

    • TGM2|TRANSGLUTAMINASE-M-V ,  BIRC2 |CIAP-R-V ,  YAP1|YAP-R-E ,  RAB11A RAB11B|RAB11-R-E ,  ESR1|ER-ALPHA-R-V ,  ...

  • No genes correlated to 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'RADIATIONS_RADIATION_REGIMENINDICATION', 'NUMBER_OF_LYMPH_NODES', 'RACE', 'ETHNICITY', 'WEIGHT_KG_AT_DIAGNOSIS', 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY', 'NEOPLASM_HISTOLOGIC_GRADE', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_HISTORY', 'PATIENT.AGEBEGANSMOKINGINYEARS', 'RADIATION_TOTAL_DOSE', 'RADIATION_THERAPY_TYPE', 'RADIATION_THERAPY_SITE', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT', 'PREGNANCIES_COUNT_ECTOPIC', 'POS_LYMPH_NODE_LOCATION', 'LYMPHOVASCULAR_INVOLVEMENT', 'LYMPH_NODES_EXAMINED_HE_COUNT', 'KERATINIZATION_SQUAMOUS_CELL', 'HEIGHT_CM_AT_DIAGNOSIS', 'CORPUS_INVOLVEMENT', 'CHEMO_CONCURRENT_TYPE', 'AJCC_TUMOR_PATHOLOGIC_PT', and 'STAGE_EVENT.CLINICAL_STAGE'.

Results
Overview of the results

Complete statistical result table is provided in Supplement Table 1

Table 1.  Get Full Table This table shows the clinical features, statistical methods used, and the number of 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
DAYS_TO_DEATH_OR_LAST_FUP Cox regression test N=10 shorter survival N=7 longer survival N=3
YEARS_TO_BIRTH Spearman correlation test N=30 older N=15 younger N=15
PATHOLOGY_T_STAGE Spearman correlation test N=8 higher stage N=4 lower stage N=4
PATHOLOGY_N_STAGE Wilcoxon test   N=0        
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
HISTOLOGICAL_TYPE Kruskal-Wallis test N=15        
RADIATIONS_RADIATION_REGIMENINDICATION Wilcoxon test   N=0        
NUMBER_PACK_YEARS_SMOKED Spearman correlation test N=30 higher number_pack_years_smoked N=12 lower number_pack_years_smoked N=18
NUMBER_OF_LYMPH_NODES Spearman correlation test   N=0        
RACE Kruskal-Wallis test   N=0        
ETHNICITY Wilcoxon test   N=0        
WEIGHT_KG_AT_DIAGNOSIS Spearman correlation test   N=0        
TUMOR_STATUS Wilcoxon test N=1 with tumor N=1 tumor free N=0
TUMOR_SAMPLE_PROCUREMENT_COUNTRY Kruskal-Wallis test   N=0        
NEOPLASM_HISTOLOGIC_GRADE Kruskal-Wallis test   N=0        
TOBACCO_SMOKING_YEAR_STOPPED Spearman correlation test   N=0        
TOBACCO_SMOKING_PACK_YEARS_SMOKED Spearman correlation test N=30 higher tobacco_smoking_pack_years_smoked N=12 lower tobacco_smoking_pack_years_smoked N=18
TOBACCO_SMOKING_HISTORY Kruskal-Wallis test   N=0        
PATIENT AGEBEGANSMOKINGINYEARS Spearman correlation test   N=0        
RADIATION_TOTAL_DOSE Spearman correlation test   N=0        
RADIATION_THERAPY_TYPE Kruskal-Wallis test   N=0        
RADIATION_THERAPY_SITE Kruskal-Wallis test   N=0        
RADIATION_ADJUVANT_UNITS Wilcoxon test N=30 gy N=30 cgy N=0
PREGNANCIES_COUNT_TOTAL Spearman correlation test   N=0        
PREGNANCIES_COUNT_STILLBIRTH Wilcoxon test   N=0        
PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT Spearman correlation test   N=0        
PREGNANCIES_COUNT_LIVE_BIRTH Spearman correlation test N=9 higher pregnancies_count_live_birth N=4 lower pregnancies_count_live_birth N=5
PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT Spearman correlation test N=7 higher patient_patientpregnancytherapeuticabortioncount N=5 lower patient_patientpregnancytherapeuticabortioncount N=2
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=0        
LYMPH_NODES_EXAMINED_HE_COUNT Spearman correlation test   N=0        
LYMPH_NODES_EXAMINED Spearman correlation test N=20 higher lymph_nodes_examined N=13 lower lymph_nodes_examined N=7
KERATINIZATION_SQUAMOUS_CELL Wilcoxon test   N=0        
INITIAL_PATHOLOGIC_DX_YEAR Spearman correlation test N=3 higher initial_pathologic_dx_year N=2 lower initial_pathologic_dx_year N=1
HISTORY_HORMONAL_CONTRACEPTIVES_USE Kruskal-Wallis test N=1        
HEIGHT_CM_AT_DIAGNOSIS Spearman correlation test   N=0        
CORPUS_INVOLVEMENT Wilcoxon test   N=0        
CHEMO_CONCURRENT_TYPE Kruskal-Wallis test   N=0        
CERVIX_SUV_RESULTS Spearman correlation test N=27 higher cervix_suv_results N=18 lower cervix_suv_results N=9
AJCC_TUMOR_PATHOLOGIC_PT Kruskal-Wallis test   N=0        
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=0        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

10 genes 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=18.4)
  censored N = 141
  death N = 30
     
  Significant markers N = 10
  associated with shorter survival 7
  associated with longer survival 3
List of 10 genes differentially expressed by 'DAYS_TO_DEATH_OR_LAST_FUP'

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

HazardRatio Wald_P Q C_index
EIF4EBP1|4E-BP1_PT70-R-V 8.2 0.001395 0.14 0.663
CCND1|CYCLIN_D1-R-V 3.5 0.001574 0.14 0.68
RAD51|RAD51-R-V 3 0.003388 0.14 0.678
PECAM1|CD31-M-V 0.13 0.003392 0.14 0.454
RAB11A RAB11B|RAB11-R-E 7.9 0.004748 0.14 0.642
BCL2|BCL-2-M-V 0.3 0.004838 0.14 0.367
SMAD3|SMAD3-R-V 31 0.005162 0.14 0.651
ERRFI1|MIG-6-M-V 19 0.005802 0.14 0.649
SFRS1|SF2-M-V 0.67 0.01355 0.28 0.327
ERBB3|HER3_PY1289-R-C 8.7 0.01448 0.28 0.625
Clinical variable #2: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

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

YEARS_TO_BIRTH Mean (SD) 47.5 (14)
  Significant markers N = 30
  pos. correlated 15
  neg. correlated 15
List of top 10 genes differentially expressed by 'YEARS_TO_BIRTH'

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

SpearmanCorr corrP Q
TGM2|TRANSGLUTAMINASE-M-V -0.3378 7.077e-06 0.00136
BIRC2 |CIAP-R-V -0.2931 0.00011 0.0103
YAP1|YAP-R-E -0.2863 0.0001607 0.0103
ESR1|ER-ALPHA-R-V 0.2713 0.0003594 0.017
RAB11A RAB11B|RAB11-R-E -0.2672 0.0004438 0.017
YAP1|YAP_PS127-R-E -0.2327 0.002328 0.0713
BAP1|BAP1-C-4-M-E 0.2286 0.002794 0.0713
BCL2L1|BCL-XL-R-V -0.2243 0.003366 0.0713
AKT1 AKT2 AKT3|AKT_PS473-R-V 0.2232 0.003537 0.0713
PEA15|PEA15-R-V -0.222 0.003715 0.0713
Clinical variable #3: 'PATHOLOGY_T_STAGE'

8 genes related to 'PATHOLOGY_T_STAGE'.

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

PATHOLOGY_T_STAGE Mean (SD) 1.39 (0.68)
  N
  T1 99
  T2 31
  T3 7
  T4 3
     
  Significant markers N = 8
  pos. correlated 4
  neg. correlated 4
List of 8 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S6.  Get Full Table List of 8 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
ANXA7 |ANNEXIN_VII-M-V -0.2426 0.003882 0.205
DVL3|DVL3-R-V 0.2414 0.004063 0.205
ERBB2|HER2_PY1248-R-C 0.2403 0.004233 0.205
PECAM1|CD31-M-V -0.2399 0.00431 0.205
SYK|SYK-M-V 0.2342 0.005351 0.205
FOXO3|FOXO3A-R-C -0.2236 0.007913 0.253
TGM2|TRANSGLUTAMINASE-M-V -0.2179 0.009692 0.266
EIF4G1|EIF4G-R-C 0.2111 0.01229 0.295
Clinical variable #4: 'PATHOLOGY_N_STAGE'

No gene related to 'PATHOLOGY_N_STAGE'.

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

PATHOLOGY_N_STAGE Labels N
  N0 92
  N1 38
     
  Significant markers N = 0
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
  class0 83
  class1 4
     
  Significant markers N = 0
Clinical variable #6: 'HISTOLOGICAL_TYPE'

15 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  ADENOSQUAMOUS 3
  CERVICAL SQUAMOUS CELL CARCINOMA 144
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA 17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE 3
     
  Significant markers N = 15
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'

kruskal_wallis_P Q
NDRG1|NDRG1_PT346-R-V 1.915e-06 0.000368
EGFR|EGFR-R-V 2.647e-05 0.00254
C12ORF5|TIGAR-R-V 5.769e-05 0.00369
XRCC1|XRCC1-R-E 0.000153 0.00734
PRKAA1|AMPK_ALPHA-R-C 0.0003718 0.0143
CLDN7|CLAUDIN-7-R-V 0.0005449 0.0174
PIK3R1|PI3K-P85-R-V 0.001214 0.0272
ESR1|ER-ALPHA_PS118-R-V 0.001215 0.0272
NOTCH1|NOTCH1-R-V 0.001273 0.0272
MAP2K1|MEK1-R-V 0.004694 0.0901
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 25
  YES 147
     
  Significant markers N = 0
Clinical variable #8: 'NUMBER_PACK_YEARS_SMOKED'

30 genes related to 'NUMBER_PACK_YEARS_SMOKED'.

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

NUMBER_PACK_YEARS_SMOKED Mean (SD) 17.69 (14)
  Significant markers N = 30
  pos. correlated 12
  neg. correlated 18
List of top 10 genes differentially expressed by 'NUMBER_PACK_YEARS_SMOKED'

Table S13.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_PACK_YEARS_SMOKED' by Spearman correlation test

SpearmanCorr corrP Q
MET|C-MET_PY1235-R-V -0.4904 0.0006258 0.0533
ARHI|ARHI-M-E -0.4864 0.0007042 0.0533
MAPK8|JNK_PT183_PY185-R-V -0.4751 0.000975 0.0533
GSK3A GSK3B|GSK3-ALPHA-BETA-M-V 0.4705 0.00111 0.0533
INPP4B|INPP4B-R-V -0.4378 0.002634 0.101
CTNNB2|BETA-CATENIN-R-V 0.426 0.003528 0.113
PDK1|PDK1_PS241-R-V 0.4184 0.004235 0.116
EGFR|EGFR_PY1173-R-V -0.4012 0.006312 0.136
MRE11A|MRE11-R-C -0.4008 0.006369 0.136
STMN1|STATHMIN-R-V -0.3891 0.008251 0.154
Clinical variable #9: 'NUMBER_OF_LYMPH_NODES'

No gene related to 'NUMBER_OF_LYMPH_NODES'.

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

NUMBER_OF_LYMPH_NODES Mean (SD) 1.15 (2.7)
  Significant markers N = 0
Clinical variable #10: 'RACE'

No gene related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 3
  ASIAN 15
  BLACK OR AFRICAN AMERICAN 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 1
  WHITE 124
     
  Significant markers N = 0
Clinical variable #11: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 13
  NOT HISPANIC OR LATINO 112
     
  Significant markers N = 0
Clinical variable #12: 'WEIGHT_KG_AT_DIAGNOSIS'

No gene related to 'WEIGHT_KG_AT_DIAGNOSIS'.

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

WEIGHT_KG_AT_DIAGNOSIS Mean (SD) 74.87 (23)
  Significant markers N = 0
Clinical variable #13: 'TUMOR_STATUS'

One gene related to 'TUMOR_STATUS'.

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

TUMOR_STATUS Labels N
  TUMOR FREE 87
  WITH TUMOR 24
     
  Significant markers N = 1
  Higher in WITH TUMOR 1
  Higher in TUMOR FREE 0
List of one gene differentially expressed by 'TUMOR_STATUS'

Table S19.  Get Full Table List of one gene differentially expressed by 'TUMOR_STATUS'

W(pos if higher in 'WITH TUMOR') wilcoxontestP Q AUC
SCD1|SCD1-M-V 600 0.001488 0.286 0.7126
Clinical variable #14: 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

No gene related to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.

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

TUMOR_SAMPLE_PROCUREMENT_COUNTRY Labels N
  BRAZIL 8
  CANADA 4
  RUSSIA 12
  UKRAINE 7
  UNITED STATES 128
  VIETNAM 13
     
  Significant markers N = 0
Clinical variable #15: 'NEOPLASM_HISTOLOGIC_GRADE'

No gene related to 'NEOPLASM_HISTOLOGIC_GRADE'.

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

NEOPLASM_HISTOLOGIC_GRADE Labels N
  G1 10
  G2 75
  G3 73
  G4 1
  GX 8
     
  Significant markers N = 0
Clinical variable #16: 'TOBACCO_SMOKING_YEAR_STOPPED'

No gene related to 'TOBACCO_SMOKING_YEAR_STOPPED'.

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

TOBACCO_SMOKING_YEAR_STOPPED Mean (SD) 2001.6 (11)
  Significant markers N = 0
Clinical variable #17: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'

30 genes related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.

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

TOBACCO_SMOKING_PACK_YEARS_SMOKED Mean (SD) 17.69 (14)
  Significant markers N = 30
  pos. correlated 12
  neg. correlated 18
List of top 10 genes differentially expressed by 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'

Table S24.  Get Full Table List of top 10 genes significantly correlated to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED' by Spearman correlation test

SpearmanCorr corrP Q
MET|C-MET_PY1235-R-V -0.4904 0.0006258 0.0533
ARHI|ARHI-M-E -0.4864 0.0007042 0.0533
MAPK8|JNK_PT183_PY185-R-V -0.4751 0.000975 0.0533
GSK3A GSK3B|GSK3-ALPHA-BETA-M-V 0.4705 0.00111 0.0533
INPP4B|INPP4B-R-V -0.4378 0.002634 0.101
CTNNB2|BETA-CATENIN-R-V 0.426 0.003528 0.113
PDK1|PDK1_PS241-R-V 0.4184 0.004235 0.116
EGFR|EGFR_PY1173-R-V -0.4012 0.006312 0.136
MRE11A|MRE11-R-C -0.4008 0.006369 0.136
STMN1|STATHMIN-R-V -0.3891 0.008251 0.154
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 27
  CURRENT REFORMED SMOKER FOR > 15 YEARS 6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED 2
  CURRENT SMOKER 23
  LIFELONG NON-SMOKER 86
     
  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) 21.52 (7.9)
  Significant markers N = 0
Clinical variable #20: 'RADIATION_TOTAL_DOSE'

No gene related to 'RADIATION_TOTAL_DOSE'.

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

RADIATION_TOTAL_DOSE Mean (SD) 3611.77 (1900)
  Significant markers N = 0
Clinical variable #21: 'RADIATION_THERAPY_TYPE'

No gene related to 'RADIATION_THERAPY_TYPE'.

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

RADIATION_THERAPY_TYPE Labels N
  COMBINATION 12
  EXTERNAL 50
  EXTERNAL BEAM 13
  IMPLANTS 1
  INTERNAL 8
     
  Significant markers N = 0
Clinical variable #22: 'RADIATION_THERAPY_SITE'

No gene related to 'RADIATION_THERAPY_SITE'.

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

RADIATION_THERAPY_SITE Labels N
  LOCAL RECURRENCE 2
  PRIMARY TUMOR FIELD 20
  REGIONAL SITE 5
     
  Significant markers N = 0
Clinical variable #23: 'RADIATION_ADJUVANT_UNITS'

30 genes related to 'RADIATION_ADJUVANT_UNITS'.

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

RADIATION_ADJUVANT_UNITS Labels N
  CGY 18
  GY 4
     
  Significant markers N = 30
  Higher in GY 30
  Higher in CGY 0
List of top 10 genes differentially expressed by 'RADIATION_ADJUVANT_UNITS'

Table S31.  Get Full Table List of top 10 genes differentially expressed by 'RADIATION_ADJUVANT_UNITS'

W(pos if higher in 'GY') wilcoxontestP Q AUC
BCL2L1|BCL-XL-R-V 68 0.00733 0.284 0.9444
MAPK9|JNK2-R-C 4 0.00733 0.284 0.9444
YWHAB|14-3-3_BETA-R-V 67 0.009422 0.284 0.9306
BRAF|B-RAF-M-C 5 0.009422 0.284 0.9306
STAT5A|STAT5-ALPHA-R-V 5 0.009422 0.284 0.9306
TP53BP1|53BP1-R-E 7 0.01526 0.284 0.9028
XRCC5|KU80-R-C 7 0.01526 0.284 0.9028
PECAM1|CD31-M-V 64 0.01923 0.284 0.8889
PIK3CA |PI3K-P110-ALPHA-R-C 8 0.01923 0.284 0.8889
SYK|SYK-M-V 8 0.01923 0.284 0.8889
Clinical variable #24: 'PREGNANCIES_COUNT_TOTAL'

No gene related to 'PREGNANCIES_COUNT_TOTAL'.

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

PREGNANCIES_COUNT_TOTAL Mean (SD) 3.65 (2.6)
  Significant markers N = 0
Clinical variable #25: 'PREGNANCIES_COUNT_STILLBIRTH'

No gene related to 'PREGNANCIES_COUNT_STILLBIRTH'.

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

PREGNANCIES_COUNT_STILLBIRTH Labels N
  class0 68
  class1 3
     
  Significant markers N = 0
Clinical variable #26: 'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

No gene related to 'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.

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

PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT Mean (SD) 0.44 (0.84)
  Value N
  0 60
  1 22
  2 4
  4 1
  5 1
     
  Significant markers N = 0
Clinical variable #27: 'PREGNANCIES_COUNT_LIVE_BIRTH'

9 genes related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

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

PREGNANCIES_COUNT_LIVE_BIRTH Mean (SD) 2.63 (1.9)
  Significant markers N = 9
  pos. correlated 4
  neg. correlated 5
List of 9 genes differentially expressed by 'PREGNANCIES_COUNT_LIVE_BIRTH'

Table S36.  Get Full Table List of 9 genes significantly correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH' by Spearman correlation test

SpearmanCorr corrP Q
ETS1|ETS-1-R-V -0.2512 0.001931 0.263
PKC|PKC-PAN_BETAII_PS660-R-V 0.2358 0.003674 0.263
DVL3|DVL3-R-V 0.231 0.004448 0.263
SYK|SYK-M-V 0.2221 0.006299 0.263
BRCA2|BRCA2-R-C -0.2173 0.00756 0.263
PTEN|PTEN-R-V 0.2086 0.01041 0.263
CDKN1B|P27_PT157-R-C -0.206 0.01142 0.263
ERRFI1|MIG-6-M-V -0.2046 0.01203 0.263
EGFR|EGFR_PY1173-R-V -0.2039 0.01233 0.263
Clinical variable #28: 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

7 genes related to 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.

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

PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT Mean (SD) 1.12 (2.2)
  Significant markers N = 7
  pos. correlated 5
  neg. correlated 2
List of 7 genes differentially expressed by 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

Table S38.  Get Full Table List of 7 genes significantly correlated to 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT' by Spearman correlation test

SpearmanCorr corrP Q
RPS6KA1|P90RSK-R-C -0.3891 0.0003609 0.0496
EGFR|EGFR_PY1173-R-V 0.371 0.0007051 0.0496
G6PD|G6PD-M-V -0.3683 0.0007749 0.0496
ARHI|ARHI-M-E 0.3219 0.003595 0.173
MYC|C-MYC-R-C 0.2979 0.007279 0.235
FOXO3|FOXO3A_PS318_S321-R-C 0.2973 0.007408 0.235
YAP1|YAP_PS127-R-E 0.2921 0.00857 0.235
Clinical variable #29: 'PREGNANCIES_COUNT_ECTOPIC'

No gene related to 'PREGNANCIES_COUNT_ECTOPIC'.

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

PREGNANCIES_COUNT_ECTOPIC Mean (SD) 0.11 (0.36)
  Value N
  0 66
  1 6
  2 1
     
  Significant markers N = 0
Clinical variable #30: 'POS_LYMPH_NODE_LOCATION'

No gene related to 'POS_LYMPH_NODE_LOCATION'.

Table S40.  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 24
  POSITIVE BLADDER MARGIN 1
  POSITIVE VAGINAL MARGIN 5
     
  Significant markers N = 0
Clinical variable #31: 'MENOPAUSE_STATUS'

6 genes related to 'MENOPAUSE_STATUS'.

Table S41.  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) 13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY) 46
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT) 78
     
  Significant markers N = 6
List of 6 genes differentially expressed by 'MENOPAUSE_STATUS'

Table S42.  Get Full Table List of 6 genes differentially expressed by 'MENOPAUSE_STATUS'

kruskal_wallis_P Q
GAPDH|GAPDH-M-C 0.001853 0.221
TGM2|TRANSGLUTAMINASE-M-V 0.002751 0.221
BIRC2 |CIAP-R-V 0.004133 0.221
CCNE1|CYCLIN_E1-M-V 0.004821 0.221
STAT5A|STAT5-ALPHA-R-V 0.006399 0.221
RICTOR|RICTOR-R-C 0.006901 0.221
Clinical variable #32: 'LYMPHOVASCULAR_INVOLVEMENT'

No gene related to 'LYMPHOVASCULAR_INVOLVEMENT'.

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

LYMPHOVASCULAR_INVOLVEMENT Labels N
  ABSENT 52
  PRESENT 59
     
  Significant markers N = 0
Clinical variable #33: 'LYMPH_NODES_EXAMINED_HE_COUNT'

No gene related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

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

LYMPH_NODES_EXAMINED_HE_COUNT Mean (SD) 1.15 (2.7)
  Significant markers N = 0
Clinical variable #34: 'LYMPH_NODES_EXAMINED'

20 genes related to 'LYMPH_NODES_EXAMINED'.

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

LYMPH_NODES_EXAMINED Mean (SD) 20.79 (12)
  Significant markers N = 20
  pos. correlated 13
  neg. correlated 7
List of top 10 genes differentially expressed by 'LYMPH_NODES_EXAMINED'

Table S46.  Get Full Table List of top 10 genes significantly correlated to 'LYMPH_NODES_EXAMINED' by Spearman correlation test

SpearmanCorr corrP Q
PCNA|PCNA-M-C 0.29 0.001254 0.125
YAP1|YAP_PS127-R-E -0.2786 0.001972 0.125
RICTOR|RICTOR-R-C -0.2724 0.002509 0.125
CDH3|P-CADHERIN-R-C 0.2713 0.002611 0.125
MYH11|MYH11-R-V -0.2615 0.003765 0.132
ERRFI1|MIG-6-M-V 0.259 0.004131 0.132
PDCD4|PDCD4-R-C -0.242 0.0075 0.206
RPS6KA1|P90RSK-R-C 0.2297 0.01126 0.213
TSC2|TUBERIN_PT1462-R-V -0.2267 0.01241 0.213
C12ORF5|TIGAR-R-V 0.2257 0.01281 0.213
Clinical variable #35: 'KERATINIZATION_SQUAMOUS_CELL'

No gene related to 'KERATINIZATION_SQUAMOUS_CELL'.

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

KERATINIZATION_SQUAMOUS_CELL Labels N
  KERATINIZING SQUAMOUS CELL CARCINOMA 39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA 75
     
  Significant markers N = 0
Clinical variable #36: 'INITIAL_PATHOLOGIC_DX_YEAR'

3 genes related to 'INITIAL_PATHOLOGIC_DX_YEAR'.

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

INITIAL_PATHOLOGIC_DX_YEAR Mean (SD) 2008.22 (5)
  Significant markers N = 3
  pos. correlated 2
  neg. correlated 1
List of 3 genes differentially expressed by 'INITIAL_PATHOLOGIC_DX_YEAR'

Table S49.  Get Full Table List of 3 genes significantly correlated to 'INITIAL_PATHOLOGIC_DX_YEAR' by Spearman correlation test

SpearmanCorr corrP Q
ASNS|ASNS-R-V -0.2759 0.0002704 0.0519
TP53|P53-R-E 0.2318 0.002353 0.168
ARHI|ARHI-M-E 0.2293 0.002629 0.168
Clinical variable #37: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

One gene related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.

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

HISTORY_HORMONAL_CONTRACEPTIVES_USE Labels N
  CURRENT USER 5
  FORMER USER 31
  NEVER USED 51
     
  Significant markers N = 1
List of one gene differentially expressed by 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

Table S51.  Get Full Table List of one gene differentially expressed by 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

kruskal_wallis_P Q
PTEN|PTEN-R-V 0.001358 0.261
Clinical variable #38: 'HEIGHT_CM_AT_DIAGNOSIS'

No gene related to 'HEIGHT_CM_AT_DIAGNOSIS'.

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

HEIGHT_CM_AT_DIAGNOSIS Mean (SD) 161.7 (7.1)
  Significant markers N = 0
Clinical variable #39: 'CORPUS_INVOLVEMENT'

No gene related to 'CORPUS_INVOLVEMENT'.

Table S53.  Basic characteristics of clinical feature: 'CORPUS_INVOLVEMENT'

CORPUS_INVOLVEMENT Labels N
  ABSENT 84
  PRESENT 11
     
  Significant markers N = 0
Clinical variable #40: 'CHEMO_CONCURRENT_TYPE'

No gene related to 'CHEMO_CONCURRENT_TYPE'.

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

CHEMO_CONCURRENT_TYPE Labels N
  CARBOPLATIN 2
  CISPLATIN 13
  OTHER 1
     
  Significant markers N = 0
Clinical variable #41: 'CERVIX_SUV_RESULTS'

27 genes related to 'CERVIX_SUV_RESULTS'.

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

CERVIX_SUV_RESULTS Mean (SD) 13.19 (8.7)
  Significant markers N = 27
  pos. correlated 18
  neg. correlated 9
List of top 10 genes differentially expressed by 'CERVIX_SUV_RESULTS'

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

SpearmanCorr corrP Q
RPS6KA1|P90RSK_PT359_S363-R-C 0.8455 0.002078 0.19
RPS6|S6_PS235_S236-R-V 0.8364 0.002565 0.19
PARK7|DJ-1-R-E -0.8182 0.003734 0.19
CDKN1B|P27-R-V -0.7818 0.007012 0.19
YBX1|YB-1_PS102-R-V 0.7636 0.009216 0.19
PDK1|PDK1-R-V -0.7545 0.01048 0.19
EGFR|EGFR_PY1068-R-C 0.7455 0.01187 0.19
PDK1|PDK1_PS241-R-V -0.7455 0.01187 0.19
PIK3R1|PI3K-P85-R-V -0.7455 0.01187 0.19
EIF4EBP1|4E-BP1_PT37_T46-R-V 0.7364 0.01338 0.19
Clinical variable #42: 'AJCC_TUMOR_PATHOLOGIC_PT'

No gene related to 'AJCC_TUMOR_PATHOLOGIC_PT'.

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

AJCC_TUMOR_PATHOLOGIC_PT Labels N
  T1A1 1
  T1B 23
  T1B1 52
  T1B2 23
  T2 3
  T2A 4
  T2A1 6
  T2A2 7
  T2B 11
  T3 1
  T3A 1
  T3B 5
  T4 3
  TIS 1
  TX 8
     
  Significant markers N = 0
Clinical variable #43: 'AGE_AT_DIAGNOSIS'

30 genes related to 'AGE_AT_DIAGNOSIS'.

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

AGE_AT_DIAGNOSIS Mean (SD) 47.67 (14)
  Significant markers N = 30
  pos. correlated 14
  neg. correlated 16
List of top 10 genes differentially expressed by 'AGE_AT_DIAGNOSIS'

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

SpearmanCorr corrP Q
TGM2|TRANSGLUTAMINASE-M-V -0.3355 6.847e-06 0.00131
BIRC2 |CIAP-R-V -0.3008 6.094e-05 0.00585
YAP1|YAP-R-E -0.2828 0.000171 0.0109
RAB11A RAB11B|RAB11-R-E -0.27 0.0003411 0.0155
ESR1|ER-ALPHA-R-V 0.2668 0.0004025 0.0155
BCL2L1|BCL-XL-R-V -0.2301 0.002394 0.0664
YAP1|YAP_PS127-R-E -0.2299 0.002419 0.0664
BAP1|BAP1-C-4-M-E 0.218 0.004068 0.0749
BAX|BAX-R-V -0.2176 0.004136 0.0749
AKT1 AKT2 AKT3|AKT_PS473-R-V 0.2145 0.004717 0.0749
Clinical variable #44: 'STAGE_EVENT.CLINICAL_STAGE'

No gene related to 'STAGE_EVENT.CLINICAL_STAGE'.

Table S60.  Basic characteristics of clinical feature: 'STAGE_EVENT.CLINICAL_STAGE'

STAGE_EVENT.CLINICAL_STAGE Labels N
  STAGE I 4
  STAGE IA 1
  STAGE IA1 1
  STAGE IA2 1
  STAGE IB 27
  STAGE IB1 48
  STAGE IB2 27
  STAGE II 4
  STAGE IIA 5
  STAGE IIA1 4
  STAGE IIA2 4
  STAGE IIB 16
  STAGE III 1
  STAGE IIIA 1
  STAGE IIIB 19
  STAGE IVA 4
  STAGE IVB 2
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 172

  • Number of genes = 192

  • Number of clinical features = 44

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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