Correlation between RPPA expression and clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1CR5SGR
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/C1CR5SGR
Overview
Introduction

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

Summary

Testing the association between 175 genes and 17 clinical features across 222 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 12 clinical features related to at least one genes.

  • 9 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • CHEK1|CHK1_PS345-R-C ,  COL6A1|COLLAGEN_VI-R-V ,  BECN1|BECLIN-G-V ,  SNAI2|SNAIL-M-C ,  |P-REX1-R-NA ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • EGFR|EGFR_PY1068-R-V ,  SNAI2|SNAIL-M-C ,  EEF2|EEF2-R-V ,  ATM|ATM-R-C ,  MAPK8|JNK_PT183_PT185-R-V ,  ...

  • 30 genes correlated to 'NEOPLASM_DISEASESTAGE'.

    • CDK1|CDK1-R-V ,  MAPK8|JNK_PT183_PT185-R-V ,  CASP3|CASPASE-3_ACTIVE-R-C ,  RAF1|C-RAF-R-V ,  PECAM1|CD31-M-V ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • AKT1S1|PRAS40_PT246-R-V ,  DIABLO|SMAC-M-V ,  CLDN7|CLAUDIN-7-R-V ,  AR|AR-R-V ,  PIK3CA |PI3K-P110-ALPHA-R-C ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • ANXA1|ANNEXIN_I-R-V ,  PTCH1|PTCH-R-C ,  SRC|SRC_PY527-R-V ,  DVL3|DVL3-R-V ,  RAF1|C-RAF_PS338-R-C ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • ANXA1|ANNEXIN_I-R-V ,  FN1|FIBRONECTIN-R-C ,  PIK3R1|PI3K-P85-R-V ,  CHEK2|CHK2-M-C ,  XIAP|XIAP-R-C ,  ...

  • 30 genes correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

    • BCL2L1|BCL-XL-R-V ,  DVL3|DVL3-R-V ,  WWTR1|TAZ_PS89-R-C ,  RAF1|C-RAF-R-V ,  C12ORF5|TIGAR-R-V ,  ...

  • 30 genes correlated to 'EXTRATHYROIDAL_EXTENSION'.

    • PIK3CA |PI3K-P110-ALPHA-R-C ,  EIF4EBP1|4E-BP1-R-V ,  BCL2|BCL-2-R-C ,  EGFR|EGFR_PY1173-R-C ,  PAI-1|PAL-1-M-C ,  ...

  • 30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

    • PTCH1|PTCH-R-C ,  MAPK14|P38_MAPK-R-C ,  DVL3|DVL3-R-V ,  ANXA1|ANNEXIN_I-R-V ,  PXN|PAXILLIN-R-V ,  ...

  • 13 genes correlated to 'MULTIFOCALITY'.

    • CDKN1B|P27_PT157-R-C ,  EIF4EBP1|4E-BP1-R-V ,  RAF1|C-RAF_PS338-R-C ,  DIABLO|SMAC-M-V ,  ERBB3|HER3_PY1298-R-C ,  ...

  • 2 genes correlated to 'TUMOR_SIZE'.

    • STAT5A|STAT5-ALPHA-R-V ,  NFKB1|NF-KB-P65_PS536-R-C

  • 4 genes correlated to 'RACE'.

    • FOXO3|FOXO3A_PS318_S321-R-C ,  |P-REX1-R-NA ,  EIF4EBP1|4E-BP1_PT70-R-C ,  CHEK1|CHK1-R-C

  • No genes correlated to 'PATHOLOGY_M_STAGE', 'GENDER', 'RADIATION_EXPOSURE', 'COMPLETENESS_OF_RESECTION', and 'ETHNICITY'.

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=9 shorter survival N=3 longer survival N=6
YEARS_TO_BIRTH Spearman correlation test N=30 older N=16 younger N=14
NEOPLASM_DISEASESTAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=14 lower stage N=16
PATHOLOGY_N_STAGE Wilcoxon test N=30 n1 N=30 n0 N=0
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
GENDER Wilcoxon test   N=0        
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
RADIATIONS_RADIATION_REGIMENINDICATION Wilcoxon test N=30 yes N=30 no N=0
RADIATION_EXPOSURE Wilcoxon test   N=0        
EXTRATHYROIDAL_EXTENSION Kruskal-Wallis test N=30        
COMPLETENESS_OF_RESECTION Kruskal-Wallis test   N=0        
NUMBER_OF_LYMPH_NODES Spearman correlation test N=30 higher number_of_lymph_nodes N=18 lower number_of_lymph_nodes N=12
MULTIFOCALITY Wilcoxon test N=13 unifocal N=13 multifocal N=0
TUMOR_SIZE Spearman correlation test N=2 higher tumor_size N=0 lower tumor_size N=2
RACE Kruskal-Wallis test N=4        
ETHNICITY Wilcoxon test   N=0        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

9 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) 0.1-158.8 (median=22.1)
  censored N = 208
  death N = 13
     
  Significant markers N = 9
  associated with shorter survival 3
  associated with longer survival 6
List of 9 genes differentially expressed by 'DAYS_TO_DEATH_OR_LAST_FUP'

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

HazardRatio Wald_P Q C_index
CHEK1|CHK1_PS345-R-C 0 0.0001175 0.021 0.202
COL6A1|COLLAGEN_VI-R-V 2.5 0.001284 0.11 0.677
BECN1|BECLIN-G-V 0.35 0.005018 0.21 0.369
SNAI2|SNAIL-M-C 27 0.005109 0.21 0.646
|P-REX1-R-NA 0.15 0.005953 0.21 0.29
PRKAA1|AMPK_PT172-R-V 0.36 0.00773 0.23 0.343
EIF4EBP1|4E-BP1_PT70-R-C 0.03 0.009351 0.23 0.27
PAI-1|PAL-1-M-C 2.7 0.01227 0.26 0.677
XIAP|XIAP-R-C 0.13 0.01356 0.26 0.385
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) 48.08 (17)
  Significant markers N = 30
  pos. correlated 16
  neg. correlated 14
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
EGFR|EGFR_PY1068-R-V 0.3019 4.653e-06 0.000618
SNAI2|SNAIL-M-C 0.2964 7.059e-06 0.000618
EEF2|EEF2-R-V -0.286 1.504e-05 0.000877
ATM|ATM-R-C -0.2807 2.188e-05 0.000957
MAPK8|JNK_PT183_PT185-R-V 0.2757 3.112e-05 0.00109
AKT1 AKT2 AKT3|AKT_PT308-R-V 0.262 7.794e-05 0.00227
AKT1 AKT2 AKT3|AKT_PS473-R-V 0.2566 0.0001102 0.00275
DVL3|DVL3-R-V -0.2508 0.0001592 0.0034
RAD50|RAD50-M-C -0.2493 0.000175 0.0034
PRKCA |PKC-ALPHA-M-V 0.2423 0.0002685 0.00429
Clinical variable #3: 'NEOPLASM_DISEASESTAGE'

30 genes related to 'NEOPLASM_DISEASESTAGE'.

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

NEOPLASM_DISEASESTAGE Labels N
  STAGE I 117
  STAGE II 33
  STAGE III 46
  STAGE IVA 20
  STAGE IVC 4
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'NEOPLASM_DISEASESTAGE'

Table S6.  Get Full Table List of top 10 genes differentially expressed by 'NEOPLASM_DISEASESTAGE'

kruskal_wallis_P Q
CDK1|CDK1-R-V 1.908e-05 0.00334
MAPK8|JNK_PT183_PT185-R-V 5.513e-05 0.00482
CASP3|CASPASE-3_ACTIVE-R-C 0.0001268 0.0074
RAF1|C-RAF-R-V 0.0003806 0.0141
PECAM1|CD31-M-V 0.0004303 0.0141
BECN1|BECLIN-G-V 0.0004848 0.0141
MSH6|MSH6-R-C 0.0006012 0.015
EGFR|EGFR_PY1068-R-V 0.001059 0.0167
AKT1 AKT2 AKT3|AKT_PS473-R-V 0.001102 0.0167
EIF4EBP1|4E-BP1_PS65-R-V 0.001123 0.0167
Clinical variable #4: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

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

PATHOLOGY_T_STAGE Mean (SD) 2.21 (0.85)
  N
  T1 51
  T2 84
  T3 75
  T4 11
     
  Significant markers N = 30
  pos. correlated 14
  neg. correlated 16
List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S8.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
AKT1S1|PRAS40_PT246-R-V -0.3195 1.234e-06 0.000216
DIABLO|SMAC-M-V 0.2737 3.708e-05 0.00304
CLDN7|CLAUDIN-7-R-V -0.2687 5.216e-05 0.00304
AR|AR-R-V -0.2449 0.0002365 0.0088
PIK3CA |PI3K-P110-ALPHA-R-C 0.2439 0.0002513 0.0088
C12ORF5|TIGAR-R-V -0.2322 5e-04 0.0146
WWTR1|TAZ-R-C -0.2248 0.0007623 0.0191
CCNE1|CYCLIN_E1-M-V 0.2222 0.0008795 0.0192
RAF1|C-RAF-R-V -0.2193 0.001034 0.0201
COL6A1|COLLAGEN_VI-R-V -0.2169 0.001176 0.0206
Clinical variable #5: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

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

PATHOLOGY_N_STAGE Labels N
  N0 98
  N1 95
     
  Significant markers N = 30
  Higher in N1 30
  Higher in N0 0
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

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

W(pos if higher in 'N1') wilcoxontestP Q AUC
ANXA1|ANNEXIN_I-R-V 6777 4.542e-08 7.95e-06 0.7279
PTCH1|PTCH-R-C 6672 2.017e-07 1.77e-05 0.7166
SRC|SRC_PY527-R-V 2729 6.935e-07 4.05e-05 0.7069
DVL3|DVL3-R-V 6555.5 9.71e-07 4.25e-05 0.7041
RAF1|C-RAF_PS338-R-C 2928 8.578e-06 0.00025 0.6855
ERBB2|HER2_PY1248-R-V 2928 8.578e-06 0.00025 0.6855
EEF2|EEF2-R-V 6346.5 1.308e-05 0.000313 0.6817
VASP|VASP-R-C 6339 1.429e-05 0.000313 0.6809
FN1|FIBRONECTIN-R-C 6299 2.273e-05 0.000442 0.6766
PXN|PAXILLIN-R-V 6267 3.27e-05 0.000572 0.6731
Clinical variable #6: 'PATHOLOGY_M_STAGE'

No gene related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 118
  class1 5
     
  Significant markers N = 0
Clinical variable #7: 'GENDER'

No gene related to 'GENDER'.

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

GENDER Labels N
  FEMALE 154
  MALE 68
     
  Significant markers N = 0
Clinical variable #8: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  OTHER SPECIFY 2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL 158
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) 52
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) 10
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

Table S14.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

kruskal_wallis_P Q
ANXA1|ANNEXIN_I-R-V 2.162e-10 3.78e-08
FN1|FIBRONECTIN-R-C 1.139e-09 9.94e-08
PIK3R1|PI3K-P85-R-V 1.703e-09 9.94e-08
CHEK2|CHK2-M-C 1.443e-07 6.31e-06
XIAP|XIAP-R-C 2.429e-07 8.44e-06
NEK7|NEK7-R-NA 2.894e-07 8.44e-06
ERCC1|ERCC1-M-C 7.334e-07 1.83e-05
PXN|PAXILLIN-R-V 8.551e-07 1.87e-05
RAF1|C-RAF_PS338-R-C 1.306e-06 2.54e-05
COL6A1|COLLAGEN_VI-R-V 3.725e-06 6.52e-05
Clinical variable #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

30 genes related to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

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

RADIATIONS_RADIATION_REGIMENINDICATION Labels N
  NO 13
  YES 209
     
  Significant markers N = 30
  Higher in YES 30
  Higher in NO 0
List of top 10 genes differentially expressed by 'RADIATIONS_RADIATION_REGIMENINDICATION'

Table S16.  Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS_RADIATION_REGIMENINDICATION'

W(pos if higher in 'YES') wilcoxontestP Q AUC
BCL2L1|BCL-XL-R-V 453 5.636e-05 0.00986 0.8333
DVL3|DVL3-R-V 533.5 0.0002432 0.0194 0.8036
WWTR1|TAZ_PS89-R-C 2143 0.0004847 0.0194 0.7887
RAF1|C-RAF-R-V 2136 0.0005444 0.0194 0.7862
C12ORF5|TIGAR-R-V 2135 0.0005534 0.0194 0.7858
XRCC1|XRCC1-R-C 612 0.0009003 0.0263 0.7748
STK11|LKB1-M-C 2036 0.002588 0.0647 0.7494
CDKN1B|P27_PT157-R-C 2015 0.003507 0.0767 0.7416
FOXO3|FOXO3A-R-C 750 0.006814 0.119 0.724
ERBB2|HER2_PY1248-R-V 1967 0.006814 0.119 0.724
Clinical variable #10: 'RADIATION_EXPOSURE'

No gene related to 'RADIATION_EXPOSURE'.

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

RADIATION_EXPOSURE Labels N
  NO 184
  YES 11
     
  Significant markers N = 0
Clinical variable #11: 'EXTRATHYROIDAL_EXTENSION'

30 genes related to 'EXTRATHYROIDAL_EXTENSION'.

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

EXTRATHYROIDAL_EXTENSION Labels N
  MINIMAL (T3) 55
  MODERATE/ADVANCED (T4A) 10
  NONE 149
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'EXTRATHYROIDAL_EXTENSION'

Table S19.  Get Full Table List of top 10 genes differentially expressed by 'EXTRATHYROIDAL_EXTENSION'

kruskal_wallis_P Q
PIK3CA |PI3K-P110-ALPHA-R-C 2.353e-05 0.00232
EIF4EBP1|4E-BP1-R-V 2.748e-05 0.00232
BCL2|BCL-2-R-C 5.105e-05 0.00232
EGFR|EGFR_PY1173-R-C 5.295e-05 0.00232
PAI-1|PAL-1-M-C 9.793e-05 0.00343
BECN1|BECLIN-G-V 0.0001491 0.00435
DIABLO|SMAC-M-V 0.0001829 0.00445
MAPT|TAU-M-C 0.0002035 0.00445
RAF1|C-RAF-R-V 0.001013 0.0187
INPP4B|INPP4B-G-C 0.001154 0.0187
Clinical variable #12: 'COMPLETENESS_OF_RESECTION'

No gene related to 'COMPLETENESS_OF_RESECTION'.

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

COMPLETENESS_OF_RESECTION Labels N
  R0 168
  R1 23
  R2 2
  RX 14
     
  Significant markers N = 0
Clinical variable #13: 'NUMBER_OF_LYMPH_NODES'

30 genes related to 'NUMBER_OF_LYMPH_NODES'.

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

NUMBER_OF_LYMPH_NODES Mean (SD) 3.48 (5.8)
  Significant markers N = 30
  pos. correlated 18
  neg. correlated 12
List of top 10 genes differentially expressed by 'NUMBER_OF_LYMPH_NODES'

Table S22.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_OF_LYMPH_NODES' by Spearman correlation test

SpearmanCorr corrP Q
PTCH1|PTCH-R-C 0.339 6.976e-06 0.00122
MAPK14|P38_MAPK-R-C 0.3213 2.177e-05 0.0019
DVL3|DVL3-R-V 0.3101 4.302e-05 0.00251
ANXA1|ANNEXIN_I-R-V 0.3026 6.704e-05 0.00293
PXN|PAXILLIN-R-V 0.2849 0.0001818 0.00636
PTGS2|COX-2-R-C 0.2784 0.0002575 0.00648
PAI-1|PAL-1-M-C 0.2783 0.0002591 0.00648
SRC|SRC_PY527-R-V -0.2733 0.0003379 0.00739
CASP9|CASPASE-9_CLEAVEDD330-R-C 0.2695 0.0004104 0.00798
VASP|VASP-R-C 0.262 0.0006024 0.0105
Clinical variable #14: 'MULTIFOCALITY'

13 genes related to 'MULTIFOCALITY'.

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

MULTIFOCALITY Labels N
  MULTIFOCAL 101
  UNIFOCAL 114
     
  Significant markers N = 13
  Higher in UNIFOCAL 13
  Higher in MULTIFOCAL 0
List of top 10 genes differentially expressed by 'MULTIFOCALITY'

Table S24.  Get Full Table List of top 10 genes differentially expressed by 'MULTIFOCALITY'

W(pos if higher in 'UNIFOCAL') wilcoxontestP Q AUC
CDKN1B|P27_PT157-R-C 4191 0.0005843 0.102 0.636
EIF4EBP1|4E-BP1-R-V 7158 0.002096 0.147 0.6217
RAF1|C-RAF_PS338-R-C 4442 0.003884 0.147 0.6142
DIABLO|SMAC-M-V 7054 0.004401 0.147 0.6126
ERBB3|HER3_PY1298-R-C 4501 0.005819 0.147 0.6091
STK11|LKB1-M-C 4501 0.005819 0.147 0.6091
ACACA|ACC1-R-C 7011 0.005897 0.147 0.6089
BAX|BAX-R-V 6971 0.007686 0.168 0.6054
CHEK2|CHK2-M-C 6886 0.01318 0.201 0.5981
CDKN1A|P21-R-C 6879.5 0.01372 0.201 0.5975
Clinical variable #15: 'TUMOR_SIZE'

2 genes related to 'TUMOR_SIZE'.

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

TUMOR_SIZE Mean (SD) 3.29 (1.6)
  Significant markers N = 2
  pos. correlated 0
  neg. correlated 2
List of 2 genes differentially expressed by 'TUMOR_SIZE'

Table S26.  Get Full Table List of 2 genes significantly correlated to 'TUMOR_SIZE' by Spearman correlation test

SpearmanCorr corrP Q
STAT5A|STAT5-ALPHA-R-V -0.215 0.002817 0.25
NFKB1|NF-KB-P65_PS536-R-C -0.2147 0.002853 0.25
Clinical variable #16: 'RACE'

4 genes related to 'RACE'.

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

RACE Labels N
  ASIAN 16
  BLACK OR AFRICAN AMERICAN 13
  WHITE 147
     
  Significant markers N = 4
List of 4 genes differentially expressed by 'RACE'

Table S28.  Get Full Table List of 4 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
FOXO3|FOXO3A_PS318_S321-R-C 0.0002052 0.0359
|P-REX1-R-NA 0.0005399 0.0472
EIF4EBP1|4E-BP1_PT70-R-C 0.001193 0.0696
CHEK1|CHK1-R-C 0.006666 0.292
Clinical variable #17: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 16
  NOT HISPANIC OR LATINO 168
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 222

  • Number of genes = 175

  • Number of clinical features = 17

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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