Correlation between RPPA expression and clinical features
Prostate Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1TD9W8D
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between RPPA expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1TD9W8D
Overview
Introduction

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

Summary

Testing the association between 189 genes and 12 clinical features across 159 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 11 clinical features related to at least one genes.

  • 1 gene correlated to 'AGE'.

    • EIF4EBP1|4E-BP1_PT37_T46-R-V

  • 13 genes correlated to 'PATHOLOGY.T.STAGE'.

    • EIF4G1|EIF4G-R-C ,  DVL3|DVL3-R-V ,  EEF2K|EEF2K-R-V ,  RBM15|RBM15-R-V ,  XRCC5|KU80-R-C ,  ...

  • 2 genes correlated to 'PATHOLOGY.N.STAGE'.

    • CDKN1B|P27_PT157-R-C ,  SQSTM1|P62-LCK-LIGAND-M-C

  • 6 genes correlated to 'COMPLETENESS.OF.RESECTION'.

    • STAT3|STAT3_PY705-R-V ,  RPS6|S6_PS240_S244-R-V ,  RPS6|S6_PS235_S236-R-V ,  MAPK1 MAPK3|MAPK_PT202_Y204-R-V ,  GSK3A GSK3B|GSK3-ALPHA-BETA_PS21_S9-R-V ,  ...

  • 2 genes correlated to 'NUMBER.OF.LYMPH.NODES'.

    • CDKN1B|P27_PT157-R-C ,  SQSTM1|P62-LCK-LIGAND-M-C

  • 17 genes correlated to 'GLEASON_SCORE_COMBINED'.

    • SHC1|SHC_PY317-R-E ,  BCL2L11|BIM-R-V ,  GAB2|GAB2-R-V ,  CDH3|P-CADHERIN-R-C ,  TFRC|TFRC-R-V ,  ...

  • 29 genes correlated to 'GLEASON_SCORE_PRIMARY'.

    • EIF4G1|EIF4G-R-C ,  CCNB1|CYCLIN_B1-R-V ,  CAV1|CAVEOLIN-1-R-V ,  ERRFI1|MIG-6-M-V ,  GSK3A GSK3B|GSK3_PS9-R-V ,  ...

  • 5 genes correlated to 'GLEASON_SCORE_SECONDARY'.

    • CDH3|P-CADHERIN-R-C ,  ADAR|ADAR1-R-V ,  RPS6KB1|P70S6K_PT389-R-V ,  BCL2L11|BIM-R-V ,  YWHAE|14-3-3_EPSILON-M-C

  • 31 genes correlated to 'GLEASON_SCORE'.

    • BCL2L11|BIM-R-V ,  EIF4G1|EIF4G-R-C ,  GAB2|GAB2-R-V ,  SHC1|SHC_PY317-R-E ,  DVL3|DVL3-R-V ,  ...

  • 5 genes correlated to 'PSA_RESULT_PREOP'.

    • EEF2|EEF2-R-C ,  RAD50|RAD50-M-V ,  PRKAA1|AMPK_PT172-R-V ,  RAF1|C-RAF-R-V ,  ACACA|ACC1-R-E

  • 2 genes correlated to 'PSA_VALUE'.

    • PEA15|PEA15-R-V ,  MYH9|MYOSIN-IIA_PS1943-R-V

  • No genes correlated to 'RACE'

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
AGE Spearman correlation test N=1 older N=1 younger N=0
PATHOLOGY T STAGE Spearman correlation test N=13 higher stage N=12 lower stage N=1
PATHOLOGY N STAGE Wilcoxon test N=2 class1 N=2 class0 N=0
COMPLETENESS OF RESECTION Kruskal-Wallis test N=6        
NUMBER OF LYMPH NODES Spearman correlation test N=2 higher number.of.lymph.nodes N=1 lower number.of.lymph.nodes N=1
GLEASON_SCORE_COMBINED Spearman correlation test N=17 higher score N=11 lower score N=6
GLEASON_SCORE_PRIMARY Spearman correlation test N=29 higher score N=11 lower score N=18
GLEASON_SCORE_SECONDARY Spearman correlation test N=5 higher score N=1 lower score N=4
GLEASON_SCORE Spearman correlation test N=31 higher score N=16 lower score N=15
PSA_RESULT_PREOP Spearman correlation test N=5 higher psa_result_preop N=5 lower psa_result_preop N=0
PSA_VALUE Spearman correlation test N=2 higher psa_value N=1 lower psa_value N=1
RACE Kruskal-Wallis test   N=0        
Clinical variable #1: 'AGE'

One gene related to 'AGE'.

Table S1.  Basic characteristics of clinical feature: 'AGE'

AGE Mean (SD) 60.58 (7.1)
  Significant markers N = 1
  pos. correlated 1
  neg. correlated 0
List of one gene differentially expressed by 'AGE'

Table S2.  Get Full Table List of one gene significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
EIF4EBP1|4E-BP1_PT37_T46-R-V 0.2518 0.001463 0.277
Clinical variable #2: 'PATHOLOGY.T.STAGE'

13 genes related to 'PATHOLOGY.T.STAGE'.

Table S3.  Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE Mean (SD) 2.66 (0.54)
  N
  2 58
  3 95
  4 5
     
  Significant markers N = 13
  pos. correlated 12
  neg. correlated 1
List of top 10 genes differentially expressed by 'PATHOLOGY.T.STAGE'

Table S4.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
EIF4G1|EIF4G-R-C 0.3667 2.15e-06 0.000406
DVL3|DVL3-R-V 0.3561 4.396e-06 0.000826
EEF2K|EEF2K-R-V 0.3379 1.413e-05 0.00264
RBM15|RBM15-R-V 0.3251 3.072e-05 0.00571
XRCC5|KU80-R-C 0.3215 3.794e-05 0.00702
GAB2|GAB2-R-V 0.2962 0.0001576 0.029
TP53BP1|53BP1-R-E 0.283 0.0003149 0.0576
BRAF|B-RAF-M-C 0.2765 0.0004364 0.0794
NOTCH1|NOTCH1-R-V 0.2692 0.0006251 0.113
EGFR|EGFR-R-V 0.2605 0.0009463 0.17
Clinical variable #3: 'PATHOLOGY.N.STAGE'

2 genes related to 'PATHOLOGY.N.STAGE'.

Table S5.  Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'

PATHOLOGY.N.STAGE Labels N
  class0 123
  class1 17
     
  Significant markers N = 2
  Higher in class1 2
  Higher in class0 0
List of 2 genes differentially expressed by 'PATHOLOGY.N.STAGE'

Table S6.  Get Full Table List of 2 genes differentially expressed by 'PATHOLOGY.N.STAGE'

W(pos if higher in 'class1') wilcoxontestP Q AUC
CDKN1B|P27_PT157-R-C 503.5 0.000551 0.104 0.7592
SQSTM1|P62-LCK-LIGAND-M-C 1559 0.001065 0.2 0.7456
Clinical variable #4: 'COMPLETENESS.OF.RESECTION'

6 genes related to 'COMPLETENESS.OF.RESECTION'.

Table S7.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 112
  R1 33
  R2 1
  RX 4
     
  Significant markers N = 6
List of 6 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

Clinical variable #5: 'NUMBER.OF.LYMPH.NODES'

2 genes related to 'NUMBER.OF.LYMPH.NODES'.

Table S9.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 0.22 (0.75)
  Value N
  0 123
  1 10
  2 3
  3 3
  6 1
     
  Significant markers N = 2
  pos. correlated 1
  neg. correlated 1
List of 2 genes differentially expressed by 'NUMBER.OF.LYMPH.NODES'

Table S10.  Get Full Table List of 2 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
CDKN1B|P27_PT157-R-C -0.2981 0.0003477 0.0657
SQSTM1|P62-LCK-LIGAND-M-C 0.2789 0.0008469 0.159
Clinical variable #6: 'GLEASON_SCORE_COMBINED'

17 genes related to 'GLEASON_SCORE_COMBINED'.

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

GLEASON_SCORE_COMBINED Mean (SD) 7.41 (0.88)
  Significant markers N = 17
  pos. correlated 11
  neg. correlated 6
List of top 10 genes differentially expressed by 'GLEASON_SCORE_COMBINED'

Table S12.  Get Full Table List of top 10 genes significantly correlated to 'GLEASON_SCORE_COMBINED' by Spearman correlation test

SpearmanCorr corrP Q
SHC1|SHC_PY317-R-E -0.37 1.59e-06 3e-04
BCL2L11|BIM-R-V 0.3605 3.048e-06 0.000573
GAB2|GAB2-R-V 0.3111 6.559e-05 0.0123
CDH3|P-CADHERIN-R-C -0.2992 0.0001276 0.0237
TFRC|TFRC-R-V 0.293 0.000178 0.0329
EGFR|EGFR_PY1068-R-C -0.2881 0.0002304 0.0424
EIF4G1|EIF4G-R-C 0.2837 0.0002903 0.0531
CAV1|CAVEOLIN-1-R-V -0.2748 0.0004555 0.0829
RPS6KB1|P70S6K_PT389-R-V -0.2741 0.0004726 0.0855
PXN|PAXILLIN-R-C 0.2645 0.0007552 0.136
Clinical variable #7: 'GLEASON_SCORE_PRIMARY'

29 genes related to 'GLEASON_SCORE_PRIMARY'.

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

GLEASON_SCORE_PRIMARY Mean (SD) 3.55 (0.58)
  Score N
  2 1
  3 76
  4 76
  5 6
     
  Significant markers N = 29
  pos. correlated 11
  neg. correlated 18
List of top 10 genes differentially expressed by 'GLEASON_SCORE_PRIMARY'

Table S14.  Get Full Table List of top 10 genes significantly correlated to 'GLEASON_SCORE_PRIMARY' by Spearman correlation test

SpearmanCorr corrP Q
EIF4G1|EIF4G-R-C 0.3435 9.311e-06 0.00176
CCNB1|CYCLIN_B1-R-V 0.3281 2.426e-05 0.00456
CAV1|CAVEOLIN-1-R-V -0.3257 2.796e-05 0.00523
ERRFI1|MIG-6-M-V 0.3174 4.575e-05 0.00851
GSK3A GSK3B|GSK3_PS9-R-V -0.3126 6.035e-05 0.0112
MAPK14|P38_PT180_Y182-R-V -0.3088 7.49e-05 0.0138
TFRC|TFRC-R-V 0.3078 7.909e-05 0.0145
ESR1|ER-ALPHA_PS118-R-V 0.2922 0.0001862 0.0339
AKT1 AKT2 AKT3|AKT_PS473-R-V -0.2905 0.0002032 0.0368
SQSTM1|P62-LCK-LIGAND-M-C 0.2892 0.0002181 0.0393
Clinical variable #8: 'GLEASON_SCORE_SECONDARY'

5 genes related to 'GLEASON_SCORE_SECONDARY'.

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

GLEASON_SCORE_SECONDARY Mean (SD) 3.86 (0.68)
  Score N
  3 49
  4 83
  5 27
     
  Significant markers N = 5
  pos. correlated 1
  neg. correlated 4
List of 5 genes differentially expressed by 'GLEASON_SCORE_SECONDARY'

Table S16.  Get Full Table List of 5 genes significantly correlated to 'GLEASON_SCORE_SECONDARY' by Spearman correlation test

SpearmanCorr corrP Q
CDH3|P-CADHERIN-R-C -0.3149 5.287e-05 0.00999
ADAR|ADAR1-R-V -0.2926 0.0001824 0.0343
RPS6KB1|P70S6K_PT389-R-V -0.269 0.0006065 0.113
BCL2L11|BIM-R-V 0.2638 0.0007814 0.145
YWHAE|14-3-3_EPSILON-M-C -0.259 0.0009781 0.181
Clinical variable #9: 'GLEASON_SCORE'

31 genes related to 'GLEASON_SCORE'.

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

GLEASON_SCORE Mean (SD) 7.46 (0.91)
  Score N
  6 10
  7 100
  8 17
  9 30
  10 2
     
  Significant markers N = 31
  pos. correlated 16
  neg. correlated 15
List of top 10 genes differentially expressed by 'GLEASON_SCORE'

Table S18.  Get Full Table List of top 10 genes significantly correlated to 'GLEASON_SCORE' by Spearman correlation test

SpearmanCorr corrP Q
BCL2L11|BIM-R-V 0.3862 4.963e-07 9.38e-05
EIF4G1|EIF4G-R-C 0.3793 8.187e-07 0.000154
GAB2|GAB2-R-V 0.3642 2.369e-06 0.000443
SHC1|SHC_PY317-R-E -0.3363 1.466e-05 0.00273
DVL3|DVL3-R-V 0.3256 2.813e-05 0.0052
TFRC|TFRC-R-V 0.3256 2.813e-05 0.0052
PXN|PAXILLIN-R-C 0.3221 3.474e-05 0.00636
RBM15|RBM15-R-V 0.3194 4.056e-05 0.00738
CCNB1|CYCLIN_B1-R-V 0.309 7.408e-05 0.0134
MAP2K1|MEK1_PS217_S221-R-V -0.3073 8.162e-05 0.0147
Clinical variable #10: 'PSA_RESULT_PREOP'

5 genes related to 'PSA_RESULT_PREOP'.

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

PSA_RESULT_PREOP Mean (SD) 11.25 (11)
  Significant markers N = 5
  pos. correlated 5
  neg. correlated 0
List of 5 genes differentially expressed by 'PSA_RESULT_PREOP'

Table S20.  Get Full Table List of 5 genes significantly correlated to 'PSA_RESULT_PREOP' by Spearman correlation test

SpearmanCorr corrP Q
EEF2|EEF2-R-C 0.3335 1.969e-05 0.00372
RAD50|RAD50-M-V 0.2802 0.0003798 0.0714
PRKAA1|AMPK_PT172-R-V 0.2625 0.0008978 0.168
RAF1|C-RAF-R-V 0.2614 0.0009416 0.175
ACACA|ACC1-R-E 0.2536 0.001349 0.25
Clinical variable #11: 'PSA_VALUE'

2 genes related to 'PSA_VALUE'.

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

PSA_VALUE Mean (SD) 1.41 (4.4)
  Significant markers N = 2
  pos. correlated 1
  neg. correlated 1
List of 2 genes differentially expressed by 'PSA_VALUE'

Table S22.  Get Full Table List of 2 genes significantly correlated to 'PSA_VALUE' by Spearman correlation test

SpearmanCorr corrP Q
PEA15|PEA15-R-V -0.2626 0.001475 0.279
MYH9|MYOSIN-IIA_PS1943-R-V 0.2625 0.001479 0.279
Clinical variable #12: 'RACE'

No gene related to 'RACE'.

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

RACE Labels N
  ASIAN 2
  BLACK OR AFRICAN AMERICAN 6
  WHITE 121
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 159

  • Number of genes = 189

  • Number of clinical features = 12

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] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[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)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle