Correlation between RPPA expression and clinical features
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 15 clinical features across 219 samples, statistically thresholded by Q value < 0.05, 10 clinical features related to at least one genes.

  • 1 gene correlated to 'Time to Death'.

    • CHEK1|CHK1_PS345-R-C

  • 10 genes correlated to 'AGE'.

    • EGFR|EGFR_PY1068-R-V ,  SNAI2|SNAIL-M-C ,  EEF2|EEF2-R-V ,  AKT1 AKT2 AKT3|AKT_PT308-R-V ,  MAPK8|JNK_PT183_PT185-R-V ,  ...

  • 5 genes correlated to 'NEOPLASM.DISEASESTAGE'.

    • BECN1|BECLIN-G-V ,  PECAM1|CD31-M-V ,  CDK1|CDK1-R-V ,  CASP3|CASPASE-3_ACTIVE-R-C ,  MAPK8|JNK_PT183_PT185-R-V

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

    • AKT1S1|PRAS40_PT246-R-V ,  CLDN7|CLAUDIN-7-R-V ,  DIABLO|SMAC-M-V ,  AR|AR-R-V

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

    • ANXA1|ANNEXIN_I-R-V ,  SRC|SRC_PY527-R-V ,  PTCH1|PTCH-R-C ,  DVL3|DVL3-R-V ,  PXN|PAXILLIN-R-V ,  ...

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

    • BCL2L1|BCL-XL-R-V ,  PECAM1|CD31-M-V

  • 29 genes correlated to 'HISTOLOGICAL.TYPE'.

    • ANXA1|ANNEXIN_I-R-V ,  FN1|FIBRONECTIN-R-C ,  PIK3R1|PI3K-P85-R-V ,  CHEK2|CHK2-M-C ,  NEK7|NEK7-R-NA ,  ...

  • 7 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

    • ERBB2|HER2_PY1248-R-V ,  DVL3|DVL3-R-V ,  MET|C-MET-M-C ,  WWTR1|TAZ_PS89-R-C ,  ARID1A|ARID1A-M-V ,  ...

  • 6 genes correlated to 'EXTRATHYROIDAL.EXTENSION'.

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

  • 6 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 ,  ...

  • No genes correlated to 'GENDER', 'RADIATIONEXPOSURE', 'COMPLETENESS.OF.RESECTION', 'MULTIFOCALITY', and 'TUMOR.SIZE'.

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 Q value < 0.05.

Clinical feature Statistical test Significant genes Associated with                 Associated with
Time to Death Cox regression test N=1 shorter survival N=0 longer survival N=1
AGE Spearman correlation test N=10 older N=6 younger N=4
NEOPLASM DISEASESTAGE ANOVA test N=5        
PATHOLOGY T STAGE Spearman correlation test N=4 higher stage N=1 lower stage N=3
PATHOLOGY N STAGE t test N=17 class1 N=14 class0 N=3
PATHOLOGY M STAGE ANOVA test N=2        
GENDER t test   N=0        
HISTOLOGICAL TYPE ANOVA test N=29        
RADIATIONS RADIATION REGIMENINDICATION t test N=7 yes N=5 no N=2
RADIATIONEXPOSURE t test   N=0        
EXTRATHYROIDAL EXTENSION ANOVA test N=6        
COMPLETENESS OF RESECTION ANOVA test   N=0        
NUMBER OF LYMPH NODES Spearman correlation test N=6 higher number.of.lymph.nodes N=6 lower number.of.lymph.nodes N=0
MULTIFOCALITY t test   N=0        
TUMOR SIZE Spearman correlation test   N=0        
Clinical variable #1: 'Time to Death'

One gene related to 'Time to Death'.

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

Time to Death Duration (Months) 0.1-158.8 (median=17.6)
  censored N = 205
  death N = 13
     
  Significant markers N = 1
  associated with shorter survival 0
  associated with longer survival 1
List of one gene significantly associated with 'Time to Death' by Cox regression test

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

HazardRatio Wald_P Q C_index
CHEK1|CHK1_PS345-R-C 0 9.576e-05 0.017 0.203

Figure S1.  Get High-res Image As an example, this figure shows the association of CHEK1|CHK1_PS345-R-C to 'Time to Death'. four curves present the cumulative survival rates of 4 quartile subsets of patients. P value = 9.58e-05 with univariate Cox regression analysis using continuous log-2 expression values.

Clinical variable #2: 'AGE'

10 genes related to 'AGE'.

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

AGE Mean (SD) 48.37 (17)
  Significant markers N = 10
  pos. correlated 6
  neg. correlated 4
List of 10 genes significantly correlated to 'AGE' by Spearman correlation test

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

SpearmanCorr corrP Q
EGFR|EGFR_PY1068-R-V 0.2913 1.181e-05 0.00207
SNAI2|SNAIL-M-C 0.2838 2.006e-05 0.00349
EEF2|EEF2-R-V -0.2803 2.556e-05 0.00442
AKT1 AKT2 AKT3|AKT_PT308-R-V 0.2788 2.853e-05 0.00491
MAPK8|JNK_PT183_PT185-R-V 0.2683 5.796e-05 0.00991
DVL3|DVL3-R-V -0.2635 7.898e-05 0.0134
ATM|ATM-R-C -0.2622 8.587e-05 0.0145
AKT1 AKT2 AKT3|AKT_PS473-R-V 0.2564 0.0001245 0.0209
RAD50|RAD50-M-C -0.2498 0.0001876 0.0313
PRKCA |PKC-ALPHA-M-V 0.2489 0.0001984 0.0329

Figure S2.  Get High-res Image As an example, this figure shows the association of EGFR|EGFR_PY1068-R-V to 'AGE'. P value = 1.18e-05 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

5 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S5.  Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 114
  STAGE II 33
  STAGE III 45
  STAGE IVA 21
  STAGE IVC 4
     
  Significant markers N = 5
List of 5 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

Table S6.  Get Full Table List of 5 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

ANOVA_P Q
BECN1|BECLIN-G-V 4.245e-07 7.43e-05
PECAM1|CD31-M-V 1.17e-05 0.00204
CDK1|CDK1-R-V 2.754e-05 0.00476
CASP3|CASPASE-3_ACTIVE-R-C 5.924e-05 0.0102
MAPK8|JNK_PT183_PT185-R-V 0.0002568 0.0439

Figure S3.  Get High-res Image As an example, this figure shows the association of BECN1|BECLIN-G-V to 'NEOPLASM.DISEASESTAGE'. P value = 4.24e-07 with ANOVA analysis.

Clinical variable #4: 'PATHOLOGY.T.STAGE'

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

Table S7.  Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE Mean (SD) 2.21 (0.86)
  N
  1 51
  2 82
  3 74
  4 11
     
  Significant markers N = 4
  pos. correlated 1
  neg. correlated 3
List of 4 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

Table S8.  Get Full Table List of 4 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
AKT1S1|PRAS40_PT246-R-V -0.3141 2.238e-06 0.000392
CLDN7|CLAUDIN-7-R-V -0.2631 8.418e-05 0.0146
DIABLO|SMAC-M-V 0.2587 0.0001117 0.0193
AR|AR-R-V -0.2534 0.0001559 0.0268

Figure S4.  Get High-res Image As an example, this figure shows the association of AKT1S1|PRAS40_PT246-R-V to 'PATHOLOGY.T.STAGE'. P value = 2.24e-06 with Spearman correlation analysis.

Clinical variable #5: 'PATHOLOGY.N.STAGE'

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

Table S9.  Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'

PATHOLOGY.N.STAGE Labels N
  class0 96
  class1 94
     
  Significant markers N = 17
  Higher in class1 14
  Higher in class0 3
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'

T(pos if higher in 'class1') ttestP Q AUC
ANXA1|ANNEXIN_I-R-V 6.43 1.268e-09 2.22e-07 0.7312
SRC|SRC_PY527-R-V -5.5 1.288e-07 2.24e-05 0.7045
PTCH1|PTCH-R-C 5.2 5.242e-07 9.07e-05 0.7169
DVL3|DVL3-R-V 5.15 6.602e-07 0.000114 0.7009
PXN|PAXILLIN-R-V 4.71 4.819e-06 0.000824 0.6721
BCL2L1|BCL-XL-R-V 4.69 5.258e-06 0.000894 0.6727
FN1|FIBRONECTIN-R-C 4.35 2.258e-05 0.00382 0.681
CASP9|CASPASE-9_CLEAVEDD330-R-C 4.25 3.486e-05 0.00586 0.6649
PTGS2|COX-2-R-C 4.21 4.027e-05 0.00672 0.6619
VASP|VASP-R-C 4.18 4.551e-05 0.00756 0.6727

Figure S5.  Get High-res Image As an example, this figure shows the association of ANXA1|ANNEXIN_I-R-V to 'PATHOLOGY.N.STAGE'. P value = 1.27e-09 with T-test analysis.

Clinical variable #6: 'PATHOLOGY.M.STAGE'

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

Table S11.  Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE Labels N
  M0 115
  M1 5
  MX 98
     
  Significant markers N = 2
List of 2 genes differentially expressed by 'PATHOLOGY.M.STAGE'

Table S12.  Get Full Table List of 2 genes differentially expressed by 'PATHOLOGY.M.STAGE'

ANOVA_P Q
BCL2L1|BCL-XL-R-V 9.138e-05 0.016
PECAM1|CD31-M-V 0.000238 0.0414

Figure S6.  Get High-res Image As an example, this figure shows the association of BCL2L1|BCL-XL-R-V to 'PATHOLOGY.M.STAGE'. P value = 9.14e-05 with ANOVA analysis.

Clinical variable #7: 'GENDER'

No gene related to 'GENDER'.

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

GENDER Labels N
  FEMALE 151
  MALE 68
     
  Significant markers N = 0
Clinical variable #8: 'HISTOLOGICAL.TYPE'

29 genes related to 'HISTOLOGICAL.TYPE'.

Table S14.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  OTHER SPECIFY 2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL 155
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) 52
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) 10
     
  Significant markers N = 29
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S15.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
ANXA1|ANNEXIN_I-R-V 4.585e-14 8.02e-12
FN1|FIBRONECTIN-R-C 1.38e-10 2.4e-08
PIK3R1|PI3K-P85-R-V 9.464e-09 1.64e-06
CHEK2|CHK2-M-C 1.061e-07 1.82e-05
NEK7|NEK7-R-NA 1.411e-07 2.41e-05
PXN|PAXILLIN-R-V 8.679e-07 0.000148
XIAP|XIAP-R-C 9.159e-07 0.000155
RAF1|C-RAF_PS338-R-C 2.205e-06 0.00037
AR|AR-R-V 3.584e-06 0.000599
ERCC1|ERCC1-M-C 3.745e-06 0.000622

Figure S7.  Get High-res Image As an example, this figure shows the association of ANXA1|ANNEXIN_I-R-V to 'HISTOLOGICAL.TYPE'. P value = 4.58e-14 with ANOVA analysis.

Clinical variable #9: 'RADIATIONS.RADIATION.REGIMENINDICATION'

7 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S16.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 13
  YES 206
     
  Significant markers N = 7
  Higher in YES 5
  Higher in NO 2
List of 7 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S17.  Get Full Table List of 7 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

T(pos if higher in 'YES') ttestP Q AUC
ERBB2|HER2_PY1248-R-V 5.02 3.892e-05 0.00681 0.724
DVL3|DVL3-R-V -5.43 4.446e-05 0.00774 0.8012
MET|C-MET-M-C 4.95 5.078e-05 0.00878 0.7058
WWTR1|TAZ_PS89-R-C 5.05 0.0001048 0.018 0.7879
ARID1A|ARID1A-M-V 4.55 0.0001437 0.0246 0.696
BCL2L1|BCL-XL-R-V -4.88 0.0002403 0.0409 0.8327
IRS1|IRS1-R-V 4.43 0.0002799 0.0473 0.7016

Figure S8.  Get High-res Image As an example, this figure shows the association of ERBB2|HER2_PY1248-R-V to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 3.89e-05 with T-test analysis.

Clinical variable #10: 'RADIATIONEXPOSURE'

No gene related to 'RADIATIONEXPOSURE'.

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

RADIATIONEXPOSURE Labels N
  NO 182
  YES 11
     
  Significant markers N = 0
Clinical variable #11: 'EXTRATHYROIDAL.EXTENSION'

6 genes related to 'EXTRATHYROIDAL.EXTENSION'.

Table S19.  Basic characteristics of clinical feature: 'EXTRATHYROIDAL.EXTENSION'

EXTRATHYROIDAL.EXTENSION Labels N
  MINIMAL (T3) 56
  MODERATE/ADVANCED (T4A) 10
  NONE 146
     
  Significant markers N = 6
List of 6 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

Table S20.  Get Full Table List of 6 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

ANOVA_P Q
EIF4EBP1|4E-BP1-R-V 1.112e-05 0.00195
PIK3CA |PI3K-P110-ALPHA-R-C 3.447e-05 0.006
BCL2|BCL-2-R-C 4.567e-05 0.0079
PAI-1|PAL-1-M-C 7.217e-05 0.0124
EGFR|EGFR_PY1173-R-C 0.0001948 0.0333
DIABLO|SMAC-M-V 0.0002322 0.0395

Figure S9.  Get High-res Image As an example, this figure shows the association of EIF4EBP1|4E-BP1-R-V to 'EXTRATHYROIDAL.EXTENSION'. P value = 1.11e-05 with ANOVA analysis.

Clinical variable #12: 'COMPLETENESS.OF.RESECTION'

No gene related to 'COMPLETENESS.OF.RESECTION'.

Table S21.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 165
  R1 23
  R2 2
  RX 14
     
  Significant markers N = 0
Clinical variable #13: 'NUMBER.OF.LYMPH.NODES'

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

Table S22.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 3.43 (5.8)
  Significant markers N = 6
  pos. correlated 6
  neg. correlated 0
List of 6 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

Table S23.  Get Full Table List of 6 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
PTCH1|PTCH-R-C 0.3566 1.941e-06 0.00034
MAPK14|P38_MAPK-R-C 0.3261 1.516e-05 0.00264
DVL3|DVL3-R-V 0.3127 3.481e-05 0.00602
ANXA1|ANNEXIN_I-R-V 0.3089 4.388e-05 0.00755
PXN|PAXILLIN-R-V 0.3015 6.792e-05 0.0116
PAI-1|PAL-1-M-C 0.2826 0.0001966 0.0334

Figure S10.  Get High-res Image As an example, this figure shows the association of PTCH1|PTCH-R-C to 'NUMBER.OF.LYMPH.NODES'. P value = 1.94e-06 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #14: 'MULTIFOCALITY'

No gene related to 'MULTIFOCALITY'.

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

MULTIFOCALITY Labels N
  MULTIFOCAL 101
  UNIFOCAL 111
     
  Significant markers N = 0
Clinical variable #15: 'TUMOR.SIZE'

No gene related to 'TUMOR.SIZE'.

Table S25.  Basic characteristics of clinical feature: 'TUMOR.SIZE'

TUMOR.SIZE Mean (SD) 3.28 (1.6)
  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 = 219

  • Number of genes = 175

  • Number of clinical features = 15

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

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

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

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.

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] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[4] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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