This pipeline uses various statistical tests to identify RPPAs whose expression levels correlated to selected clinical features.
Testing the association between 174 genes and 8 clinical features across 212 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.

1 gene correlated to 'Time to Death'.

SMAD3SMAD3RV

2 genes correlated to 'GENDER'.

MAPK14P38_PT180_Y182RV , PTGS2COX2RC

6 genes correlated to 'PATHOLOGY.T'.

MAPK1 MAPK3MAPK_PT202_Y204RV , RPS6S6_PS235_S236RV , AKT1 AKT2 AKT3AKT_PS473RV , MAPK14P38_PT180_Y182RV , SRCSRC_PY527RV , ...

3 genes correlated to 'PATHOLOGY.N'.

SRCSRC_PY416RC , ANXA1ANNEXIN_IRV , YAP1YAP_PS127RC

3 genes correlated to 'TUMOR.STAGE'.

MAPK1 MAPK3MAPK_PT202_Y204RV , RPS6S6_PS235_S236RV , ARID1AARID1AMV

No genes correlated to 'AGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'NEOADJUVANT.THERAPY'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature  Statistical test  Significant genes  Associated with  Associated with  

Time to Death  Cox regression test  N=1  shorter survival  N=1  longer survival  N=0 
AGE  Spearman correlation test  N=0  
GENDER  t test  N=2  male  N=1  female  N=1 
PATHOLOGY T  Spearman correlation test  N=6  higher pT  N=1  lower pT  N=5 
PATHOLOGY N  Spearman correlation test  N=3  higher pN  N=0  lower pN  N=3 
TUMOR STAGE  Spearman correlation test  N=3  higher stage  N=1  lower stage  N=2 
RADIATIONS RADIATION REGIMENINDICATION  t test  N=0  
NEOADJUVANT THERAPY  t test  N=0 
Time to Death  Duration (Months)  0.1210.9 (median=13.2) 
censored  N = 105  
death  N = 107  
Significant markers  N = 1  
associated with shorter survival  1  
associated with longer survival  0 
HazardRatio  Wald_P  Q  C_index  

SMAD3SMAD3RV  3.5  0.0001519  0.026  0.581 
AGE  Mean (SD)  62.12 (12) 
Significant markers  N = 0 
GENDER  Labels  N 
FEMALE  62  
MALE  150  
Significant markers  N = 2  
Higher in MALE  1  
Higher in FEMALE  1 
T(pos if higher in 'MALE')  ttestP  Q  AUC  

MAPK14P38_PT180_Y182RV  3.89  0.0001658  0.0289  0.6641 
PTGS2COX2RC  3.85  0.0001671  0.0289  0.6258 
PATHOLOGY.T  Mean (SD)  2.97 (0.97) 
N  
T1  13  
T2  59  
T3  53  
T4  79  
Significant markers  N = 6  
pos. correlated  1  
neg. correlated  5 
SpearmanCorr  corrP  Q  

MAPK1 MAPK3MAPK_PT202_Y204RV  0.3357  9.18e07  0.00016 
RPS6S6_PS235_S236RV  0.3082  7.28e06  0.00126 
AKT1 AKT2 AKT3AKT_PS473RV  0.2946  1.895e05  0.00326 
MAPK14P38_PT180_Y182RV  0.2753  6.742e05  0.0115 
SRCSRC_PY527RV  0.2737  7.472e05  0.0127 
ARID1AARID1AMV  0.2583  0.0001914  0.0324 
PATHOLOGY.N  Mean (SD)  1.08 (0.98) 
N  
N0  73  
N1  20  
N2  79  
N3  4  
Significant markers  N = 3  
pos. correlated  0  
neg. correlated  3 
SpearmanCorr  corrP  Q  

SRCSRC_PY416RC  0.3346  5.657e06  0.000984 
ANXA1ANNEXIN_IRV  0.333  6.325e06  0.00109 
YAP1YAP_PS127RC  0.2977  5.998e05  0.0103 
TUMOR.STAGE  Mean (SD)  3.32 (0.94) 
N  
Stage 1  9  
Stage 2  39  
Stage 3  31  
Stage 4  121  
Significant markers  N = 3  
pos. correlated  1  
neg. correlated  2 
SpearmanCorr  corrP  Q  

MAPK1 MAPK3MAPK_PT202_Y204RV  0.279  6.297e05  0.011 
RPS6S6_PS235_S236RV  0.2744  8.411e05  0.0146 
ARID1AARID1AMV  0.2711  0.0001032  0.0177 
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION  Labels  N 
NO  56  
YES  156  
Significant markers  N = 0 

Expresson data file = HNSC.rppa.txt

Clinical data file = HNSC.clin.merged.picked.txt

Number of patients = 212

Number of genes = 174

Number of clinical features = 8
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. KaplanMeier survival curves were plot using the four quartile subgroups of patients based on expression levels
For continuous numerical clinical features, Spearman's rank correlation coefficients (Spearman 1904) and twotailed P values were estimated using 'cor.test' function in R
For twoclass clinical features, twotailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2expression levels between the two clinical classes using 't.test' function in R
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.