Correlation between RPPA expression and clinical features
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between RPPA expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C11N80G7
Overview
Introduction

This pipeline uses various statistical tests to identify RPPAs whose expression levels correlated to selected clinical features. The input file "CESC-TP.rppa.txt" is generated in the pipeline RPPA_AnnotateWithGene in the stddata run.

Summary

Testing the association between 192 genes and 38 clinical features across 173 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 13 clinical features related to at least one genes.

  • 2 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • CDH2|N-CADHERIN ,  CCND1|CYCLIN_D1

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

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

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • NDRG1|NDRG1_PT346 ,  EGFR|EGFR ,  C12ORF5|TIGAR ,  XRCC1|XRCC1 ,  CLDN7|CLAUDIN-7 ,  ...

  • 30 genes correlated to 'NUMBER_PACK_YEARS_SMOKED'.

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

  • 1 gene correlated to 'TUMOR_STATUS'.

    • SCD1|SCD1

  • 30 genes correlated to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.

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

  • 14 genes correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

    • ETS1|ETS-1 ,  PKC|PKC-PAN_BETAII_PS660 ,  DVL3|DVL3 ,  SYK|SYK ,  BRCA2|BRCA2 ,  ...

  • 7 genes correlated to 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT'.

    • G6PD|G6PD ,  RPS6KA1|P90RSK ,  EGFR|EGFR_PY1173 ,  YAP1|YAP_PS127 ,  ARHI|ARHI ,  ...

  • 12 genes correlated to 'MENOPAUSE_STATUS'.

    • GAPDH|GAPDH ,  STAT5A|STAT5-ALPHA ,  CCNE1|CYCLIN_E1 ,  RICTOR|RICTOR ,  TGM2|TRANSGLUTAMINASE ,  ...

  • 17 genes correlated to 'LYMPH_NODES_EXAMINED'.

    • PCNA|PCNA ,  YAP1|YAP_PS127 ,  RICTOR|RICTOR ,  CDH3|P-CADHERIN ,  MYH11|MYH11 ,  ...

  • 5 genes correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.

    • ASNS|ASNS ,  TP53|P53 ,  ARHI|ARHI ,  EGFR|EGFR_PY1173 ,  MET|C-MET_PY1235

  • 27 genes correlated to 'CERVIX_SUV_RESULTS'.

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

  • 30 genes correlated to 'AGE_AT_DIAGNOSIS'.

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

  • No genes correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'RADIATION_THERAPY', 'NUMBER_OF_LYMPH_NODES', 'RACE', 'ETHNICITY', 'WEIGHT_KG_AT_DIAGNOSIS', 'NEOPLASM_HISTOLOGIC_GRADE', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_HISTORY', 'AGEBEGANSMOKINGINYEARS', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT', 'PREGNANCIES_COUNT_ECTOPIC', 'POS_LYMPH_NODE_LOCATION', 'LYMPHOVASCULAR_INVOLVEMENT', 'LYMPH_NODES_EXAMINED_HE_COUNT', 'KERATINIZATION_SQUAMOUS_CELL', 'HISTORY_HORMONAL_CONTRACEPTIVES_USE', 'HEIGHT_CM_AT_DIAGNOSIS', 'CORPUS_INVOLVEMENT', 'CHEMO_CONCURRENT_TYPE', and '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=2   N=NA   N=NA
YEARS_TO_BIRTH Spearman correlation test N=30 older N=14 younger N=16
PATHOLOGY_T_STAGE Spearman correlation test   N=0        
PATHOLOGY_N_STAGE Wilcoxon test   N=0        
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
RADIATION_THERAPY Wilcoxon test   N=0        
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
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
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 Spearman correlation test   N=0        
AGEBEGANSMOKINGINYEARS Spearman correlation test   N=0        
PREGNANCIES_COUNT_TOTAL Spearman correlation test   N=0        
PREGNANCIES_COUNT_STILLBIRTH Wilcoxon test   N=0        
PREGNANCY_SPONTANEOUS_ABORTION_COUNT Spearman correlation test   N=0        
PREGNANCIES_COUNT_LIVE_BIRTH Spearman correlation test N=14 higher pregnancies_count_live_birth N=5 lower pregnancies_count_live_birth N=9
PREGNANCY_THERAPEUTIC_ABORTION_COUNT Spearman correlation test N=7 higher pregnancy_therapeutic_abortion_count N=5 lower pregnancy_therapeutic_abortion_count 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=12        
LYMPHOVASCULAR_INVOLVEMENT Wilcoxon test   N=0        
LYMPH_NODES_EXAMINED_HE_COUNT Spearman correlation test   N=0        
LYMPH_NODES_EXAMINED Spearman correlation test N=17 higher lymph_nodes_examined N=11 lower lymph_nodes_examined N=6
KERATINIZATION_SQUAMOUS_CELL Wilcoxon test   N=0        
INITIAL_PATHOLOGIC_DX_YEAR Spearman correlation test N=5 higher initial_pathologic_dx_year N=4 lower initial_pathologic_dx_year N=1
HISTORY_HORMONAL_CONTRACEPTIVES_USE Kruskal-Wallis test   N=0        
HEIGHT_CM_AT_DIAGNOSIS Spearman correlation test   N=0        
CORPUS_INVOLVEMENT Wilcoxon test   N=0        
CHEMO_CONCURRENT_TYPE Kruskal-Wallis test   N=0        
CERVIX_SUV_RESULTS Spearman correlation test N=27 higher cervix_suv_results N=18 lower cervix_suv_results N=9
AGE_AT_DIAGNOSIS Spearman correlation test N=30 higher age_at_diagnosis N=13 lower age_at_diagnosis N=17
CLINICAL_STAGE Kruskal-Wallis test   N=0        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

2 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) 0.1-210.7 (median=22.6)
  censored N = 141
  death N = 31
     
  Significant markers N = 2
  associated with shorter survival NA
  associated with longer survival NA
List of 2 genes differentially expressed by 'DAYS_TO_DEATH_OR_LAST_FUP'

Table S2.  Get Full Table List of 2 genes significantly associated with 'Time to Death' by Cox regression test. For the survival curves, it compared quantile intervals at c(0, 0.25, 0.50, 0.75, 1) and did not try survival analysis if there is only one interval.

logrank_P Q C_index
CDH2|N-CADHERIN 0.00026 0.05 0.639
CCND1|CYCLIN_D1 0.00083 0.08 0.688
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) 47.54 (14)
  Significant markers N = 30
  pos. correlated 14
  neg. correlated 16
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 -0.3402 5.29e-06 0.00102
BIRC2 |CIAP -0.2941 9.436e-05 0.00761
YAP1|YAP -0.2901 0.0001189 0.00761
ESR1|ER-ALPHA 0.27 0.0003553 0.0171
RAB11A RAB11B|RAB11 -0.2624 0.0005257 0.0202
YAP1|YAP_PS127 -0.2367 0.001825 0.0584
PEA15|PEA15 -0.2257 0.002992 0.0693
BAP1|BAP1-C-4 0.2233 0.003326 0.0693
BCL2L1|BCL-XL -0.2229 0.00339 0.0693
AKT1 AKT2 AKT3|AKT_PS473 0.2214 0.003611 0.0693
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) 1.39 (0.68)
  N
  T1 99
  T2 32
  T3 7
  T4 3
     
  Significant markers N = 0
Clinical variable #4: 'PATHOLOGY_N_STAGE'

No gene related to 'PATHOLOGY_N_STAGE'.

Table S6.  Basic characteristics of clinical feature: 'PATHOLOGY_N_STAGE'

PATHOLOGY_N_STAGE Labels N
  N0 93
  N1 38
     
  Significant markers N = 0
Clinical variable #5: 'PATHOLOGY_M_STAGE'

No gene related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 84
  class1 4
     
  Significant markers N = 0
Clinical variable #6: 'RADIATION_THERAPY'

No gene related to 'RADIATION_THERAPY'.

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

RADIATION_THERAPY Labels N
  NO 26
  YES 60
     
  Significant markers N = 0
Clinical variable #7: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  ADENOSQUAMOUS 4
  CERVICAL SQUAMOUS CELL CARCINOMA 144
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA 16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE 4
     
  Significant markers N = 30
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 1.683e-06 0.000323
EGFR|EGFR 1.348e-05 0.00129
C12ORF5|TIGAR 4.467e-05 0.00286
XRCC1|XRCC1 0.0001784 0.00856
CLDN7|CLAUDIN-7 0.0004813 0.0185
NOTCH1|NOTCH1 0.001549 0.0496
PRKAA1|AMPK_ALPHA 0.002044 0.0505
ESR1|ER-ALPHA_PS118 0.002104 0.0505
PIK3R1|PI3K-P85 0.002682 0.0572
MAP2K1|MEK1 0.003676 0.0706
Clinical variable #8: 'NUMBER_PACK_YEARS_SMOKED'

30 genes related to 'NUMBER_PACK_YEARS_SMOKED'.

Table S11.  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 S12.  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 -0.4904 0.0006258 0.0533
ARHI|ARHI -0.4864 0.0007042 0.0533
MAPK8|JNK_PT183_PY185 -0.4751 0.000975 0.0533
GSK3A GSK3B|GSK3-ALPHA-BETA 0.4705 0.00111 0.0533
INPP4B|INPP4B -0.4378 0.002634 0.101
CTNNB2|BETA-CATENIN 0.426 0.003528 0.113
PDK1|PDK1_PS241 0.4184 0.004235 0.116
EGFR|EGFR_PY1173 -0.4012 0.006312 0.136
MRE11A|MRE11 -0.4008 0.006369 0.136
STMN1|STATHMIN -0.3891 0.008251 0.154
Clinical variable #9: 'NUMBER_OF_LYMPH_NODES'

No gene related to 'NUMBER_OF_LYMPH_NODES'.

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

NUMBER_OF_LYMPH_NODES Mean (SD) 1.14 (2.7)
  Significant markers N = 0
Clinical variable #10: 'RACE'

No gene related to 'RACE'.

Table S14.  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 125
     
  Significant markers N = 0
Clinical variable #11: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 13
  NOT HISPANIC OR LATINO 113
     
  Significant markers N = 0
Clinical variable #12: 'WEIGHT_KG_AT_DIAGNOSIS'

No gene related to 'WEIGHT_KG_AT_DIAGNOSIS'.

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

WEIGHT_KG_AT_DIAGNOSIS Mean (SD) 74.66 (23)
  Significant markers N = 0
Clinical variable #13: 'TUMOR_STATUS'

One gene related to 'TUMOR_STATUS'.

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

TUMOR_STATUS Labels N
  TUMOR FREE 119
  WITH TUMOR 36
     
  Significant markers N = 1
  Higher in WITH TUMOR 1
  Higher in TUMOR FREE 0
List of one gene differentially expressed by 'TUMOR_STATUS'

Table S18.  Get Full Table List of one gene differentially expressed by 'TUMOR_STATUS'

W(pos if higher in 'WITH TUMOR') wilcoxontestP Q AUC
SCD1|SCD1 1368 0.001047 0.201 0.6807
Clinical variable #14: 'NEOPLASM_HISTOLOGIC_GRADE'

No gene related to 'NEOPLASM_HISTOLOGIC_GRADE'.

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

NEOPLASM_HISTOLOGIC_GRADE Labels N
  G1 10
  G2 75
  G3 74
  G4 1
  GX 8
     
  Significant markers N = 0
Clinical variable #15: 'TOBACCO_SMOKING_YEAR_STOPPED'

No gene related to 'TOBACCO_SMOKING_YEAR_STOPPED'.

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

TOBACCO_SMOKING_YEAR_STOPPED Mean (SD) 2001.55 (11)
  Significant markers N = 0
Clinical variable #16: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'

30 genes related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.

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

TOBACCO_SMOKING_PACK_YEARS_SMOKED Mean (SD) 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 S22.  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 -0.4904 0.0006258 0.0533
ARHI|ARHI -0.4864 0.0007042 0.0533
MAPK8|JNK_PT183_PY185 -0.4751 0.000975 0.0533
GSK3A GSK3B|GSK3-ALPHA-BETA 0.4705 0.00111 0.0533
INPP4B|INPP4B -0.4378 0.002634 0.101
CTNNB2|BETA-CATENIN 0.426 0.003528 0.113
PDK1|PDK1_PS241 0.4184 0.004235 0.116
EGFR|EGFR_PY1173 -0.4012 0.006312 0.136
MRE11A|MRE11 -0.4008 0.006369 0.136
STMN1|STATHMIN -0.3891 0.008251 0.154
Clinical variable #17: 'TOBACCO_SMOKING_HISTORY'

No gene related to 'TOBACCO_SMOKING_HISTORY'.

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

TOBACCO_SMOKING_HISTORY Mean (SD) 1.88 (1.2)
  Value N
  1 86
  2 23
  3 6
  4 28
  5 2
     
  Significant markers N = 0
Clinical variable #18: 'AGEBEGANSMOKINGINYEARS'

No gene related to 'AGEBEGANSMOKINGINYEARS'.

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

AGEBEGANSMOKINGINYEARS Mean (SD) 21.52 (7.9)
  Significant markers N = 0
Clinical variable #19: 'PREGNANCIES_COUNT_TOTAL'

No gene related to 'PREGNANCIES_COUNT_TOTAL'.

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

PREGNANCIES_COUNT_TOTAL Mean (SD) 3.63 (2.6)
  Significant markers N = 0
Clinical variable #20: 'PREGNANCIES_COUNT_STILLBIRTH'

No gene related to 'PREGNANCIES_COUNT_STILLBIRTH'.

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

PREGNANCIES_COUNT_STILLBIRTH Labels N
  class0 69
  class1 3
     
  Significant markers N = 0
Clinical variable #21: 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT'

No gene related to 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT'.

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

PREGNANCY_SPONTANEOUS_ABORTION_COUNT Mean (SD) 0.44 (0.84)
  Value N
  0 61
  1 22
  2 4
  4 1
  5 1
     
  Significant markers N = 0
Clinical variable #22: 'PREGNANCIES_COUNT_LIVE_BIRTH'

14 genes related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

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

PREGNANCIES_COUNT_LIVE_BIRTH Mean (SD) 2.62 (1.9)
  Significant markers N = 14
  pos. correlated 5
  neg. correlated 9
List of top 10 genes differentially expressed by 'PREGNANCIES_COUNT_LIVE_BIRTH'

Table S29.  Get Full Table List of top 10 genes significantly correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH' by Spearman correlation test

SpearmanCorr corrP Q
ETS1|ETS-1 -0.2593 0.001302 0.183
PKC|PKC-PAN_BETAII_PS660 0.2455 0.002375 0.183
DVL3|DVL3 0.2401 0.002982 0.183
SYK|SYK 0.2318 0.00418 0.183
BRCA2|BRCA2 -0.2265 0.005165 0.183
PTEN|PTEN 0.2182 0.007104 0.183
CDKN1B|P27_PT157 -0.2152 0.007964 0.183
ERRFI1|MIG-6 -0.2142 0.008254 0.183
EGFR|EGFR_PY1173 -0.2132 0.008568 0.183
EIF4EBP1|4E-BP1_PT70 -0.2059 0.01122 0.215
Clinical variable #23: 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT'

7 genes related to 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT'.

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

PREGNANCY_THERAPEUTIC_ABORTION_COUNT Mean (SD) 1.11 (2.2)
  Significant markers N = 7
  pos. correlated 5
  neg. correlated 2
List of 7 genes differentially expressed by 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT'

Table S31.  Get Full Table List of 7 genes significantly correlated to 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT' by Spearman correlation test

SpearmanCorr corrP Q
G6PD|G6PD -0.3765 0.0005327 0.0587
RPS6KA1|P90RSK -0.3727 0.0006116 0.0587
EGFR|EGFR_PY1173 0.3486 0.001424 0.0911
YAP1|YAP_PS127 0.3022 0.00611 0.243
ARHI|ARHI 0.2992 0.006653 0.243
FOXO3|FOXO3A_PS318_S321 0.2946 0.007602 0.243
MYC|C-MYC 0.2819 0.01078 0.296
Clinical variable #24: 'PREGNANCIES_COUNT_ECTOPIC'

No gene related to 'PREGNANCIES_COUNT_ECTOPIC'.

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

PREGNANCIES_COUNT_ECTOPIC Mean (SD) 0.11 (0.35)
  Value N
  0 67
  1 6
  2 1
     
  Significant markers N = 0
Clinical variable #25: 'POS_LYMPH_NODE_LOCATION'

No gene related to 'POS_LYMPH_NODE_LOCATION'.

Table S33.  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 25
  POSITIVE BLADDER MARGIN 1
  POSITIVE VAGINAL MARGIN 7
     
  Significant markers N = 0
Clinical variable #26: 'MENOPAUSE_STATUS'

12 genes related to 'MENOPAUSE_STATUS'.

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

MENOPAUSE_STATUS Labels N
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL) 3
  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) 79
     
  Significant markers N = 12
List of top 10 genes differentially expressed by 'MENOPAUSE_STATUS'

Table S35.  Get Full Table List of top 10 genes differentially expressed by 'MENOPAUSE_STATUS'

kruskal_wallis_P Q
GAPDH|GAPDH 0.001699 0.26
STAT5A|STAT5-ALPHA 0.002706 0.26
CCNE1|CYCLIN_E1 0.005602 0.289
RICTOR|RICTOR 0.008359 0.289
TGM2|TRANSGLUTAMINASE 0.009827 0.289
BIRC2 |CIAP 0.01061 0.289
MRE11A|MRE11 0.01094 0.289
CDKN1B|P27_PT157 0.01348 0.289
SERPINE1|PAI-1 0.01354 0.289
CHEK2|CHK2_PT68 0.01585 0.289
Clinical variable #27: 'LYMPHOVASCULAR_INVOLVEMENT'

No gene related to 'LYMPHOVASCULAR_INVOLVEMENT'.

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

LYMPHOVASCULAR_INVOLVEMENT Labels N
  ABSENT 52
  PRESENT 60
     
  Significant markers N = 0
Clinical variable #28: 'LYMPH_NODES_EXAMINED_HE_COUNT'

No gene related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

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

LYMPH_NODES_EXAMINED_HE_COUNT Mean (SD) 1.14 (2.7)
  Significant markers N = 0
Clinical variable #29: 'LYMPH_NODES_EXAMINED'

17 genes related to 'LYMPH_NODES_EXAMINED'.

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

LYMPH_NODES_EXAMINED Mean (SD) 20.77 (12)
  Significant markers N = 17
  pos. correlated 11
  neg. correlated 6
List of top 10 genes differentially expressed by 'LYMPH_NODES_EXAMINED'

Table S39.  Get Full Table List of top 10 genes significantly correlated to 'LYMPH_NODES_EXAMINED' by Spearman correlation test

SpearmanCorr corrP Q
PCNA|PCNA 0.2875 0.001324 0.129
YAP1|YAP_PS127 -0.2755 0.002133 0.129
RICTOR|RICTOR -0.2732 0.002327 0.129
CDH3|P-CADHERIN 0.2695 0.002685 0.129
MYH11|MYH11 -0.2597 0.003871 0.144
ERRFI1|MIG-6 0.2556 0.004491 0.144
PDCD4|PDCD4 -0.2396 0.007855 0.213
RPS6KA1|P90RSK 0.2284 0.01138 0.213
TSC2|TUBERIN_PT1462 -0.2264 0.01216 0.213
C12ORF5|TIGAR 0.2257 0.01243 0.213
Clinical variable #30: 'KERATINIZATION_SQUAMOUS_CELL'

No gene related to 'KERATINIZATION_SQUAMOUS_CELL'.

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

KERATINIZATION_SQUAMOUS_CELL Labels N
  KERATINIZING SQUAMOUS CELL CARCINOMA 39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA 76
     
  Significant markers N = 0
Clinical variable #31: 'INITIAL_PATHOLOGIC_DX_YEAR'

5 genes related to 'INITIAL_PATHOLOGIC_DX_YEAR'.

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

INITIAL_PATHOLOGIC_DX_YEAR Mean (SD) 2008.25 (5)
  Significant markers N = 5
  pos. correlated 4
  neg. correlated 1
List of 5 genes differentially expressed by 'INITIAL_PATHOLOGIC_DX_YEAR'

Table S42.  Get Full Table List of 5 genes significantly correlated to 'INITIAL_PATHOLOGIC_DX_YEAR' by Spearman correlation test

SpearmanCorr corrP Q
ASNS|ASNS -0.258 0.0006576 0.0993
TP53|P53 0.2425 0.001396 0.0993
ARHI|ARHI 0.2402 0.001551 0.0993
EGFR|EGFR_PY1173 0.2179 0.004196 0.201
MET|C-MET_PY1235 0.2086 0.006187 0.238
Clinical variable #32: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

No gene related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.

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

HISTORY_HORMONAL_CONTRACEPTIVES_USE Labels N
  CURRENT USER 5
  FORMER USER 32
  NEVER USED 51
     
  Significant markers N = 0
Clinical variable #33: 'HEIGHT_CM_AT_DIAGNOSIS'

No gene related to 'HEIGHT_CM_AT_DIAGNOSIS'.

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

HEIGHT_CM_AT_DIAGNOSIS Mean (SD) 161.69 (7.1)
  Significant markers N = 0
Clinical variable #34: 'CORPUS_INVOLVEMENT'

No gene related to 'CORPUS_INVOLVEMENT'.

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

CORPUS_INVOLVEMENT Labels N
  ABSENT 84
  PRESENT 12
     
  Significant markers N = 0
Clinical variable #35: 'CHEMO_CONCURRENT_TYPE'

No gene related to 'CHEMO_CONCURRENT_TYPE'.

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

CHEMO_CONCURRENT_TYPE Labels N
  CARBOPLATIN 3
  CISPLATIN 48
  OTHER 1
     
  Significant markers N = 0
Clinical variable #36: 'CERVIX_SUV_RESULTS'

27 genes related to 'CERVIX_SUV_RESULTS'.

Table S47.  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 S48.  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 0.8455 0.002078 0.19
RPS6|S6_PS235_S236 0.8364 0.002565 0.19
PARK7|DJ-1 -0.8182 0.003734 0.19
CDKN1B|P27 -0.7818 0.007012 0.19
YBX1|YB-1_PS102 0.7636 0.009216 0.19
PDK1|PDK1 -0.7545 0.01048 0.19
EGFR|EGFR_PY1068 0.7455 0.01187 0.19
PDK1|PDK1_PS241 -0.7455 0.01187 0.19
PIK3R1|PI3K-P85 -0.7455 0.01187 0.19
EIF4EBP1|4E-BP1_PT37_T46 0.7364 0.01338 0.19
Clinical variable #37: 'AGE_AT_DIAGNOSIS'

30 genes related to 'AGE_AT_DIAGNOSIS'.

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

AGE_AT_DIAGNOSIS Mean (SD) 47.69 (14)
  Significant markers N = 30
  pos. correlated 13
  neg. correlated 17
List of top 10 genes differentially expressed by 'AGE_AT_DIAGNOSIS'

Table S50.  Get Full Table List of top 10 genes significantly correlated to 'AGE_AT_DIAGNOSIS' by Spearman correlation test

SpearmanCorr corrP Q
TGM2|TRANSGLUTAMINASE -0.3379 5.459e-06 0.00105
BIRC2 |CIAP -0.3013 5.632e-05 0.00541
YAP1|YAP -0.2842 0.0001512 0.00967
ESR1|ER-ALPHA 0.2651 0.0004239 0.017
RAB11A RAB11B|RAB11 -0.2642 0.0004435 0.017
YAP1|YAP_PS127 -0.2326 0.002073 0.0664
BCL2L1|BCL-XL -0.2284 0.002508 0.0688
BAX|BAX -0.2153 0.004439 0.0807
PEA15|PEA15 -0.2127 0.004957 0.0807
BAP1|BAP1-C-4 0.2116 0.005188 0.0807
Clinical variable #38: 'CLINICAL_STAGE'

No gene related to 'CLINICAL_STAGE'.

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

CLINICAL_STAGE Labels N
  STAGE I 4
  STAGE IA 1
  STAGE IA1 1
  STAGE IA2 1
  STAGE IB 27
  STAGE IB1 48
  STAGE IB2 28
  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 = 173

  • Number of genes = 192

  • Number of clinical features = 38

Selected clinical features
  • Further details on clinical features selected for this analysis, please find a documentation on selected CDEs (Clinical Data Elements). The first column of the file is a formula to convert values and the second column is a clinical parameter name.

  • 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, logrank test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values comparing quantile intervals using the 'coxph' function in R. Kaplan-Meier survival curves were plotted using quantile intervals at c(0, 0.25, 0.50, 0.75, 1). If there is only one interval group, it will not try survival analysis.

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)