This pipeline uses various statistical tests to identify RPPAs whose expression levels correlated to selected clinical features.
Testing the association between 166 genes and 4 clinical features across 200 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.

16 genes correlated to 'HISTOLOGICAL.TYPE'.

TP53P53RV , CHEK2CHK2_PT68RC , AKT1 AKT2 AKT3AKT_PS473RV , PGRPRRV , CDC2CDK1RV , ...

1 gene correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

CHEK1CHK1_PS345RC

No genes correlated to 'Time to Death', and 'AGE'.
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=0  
AGE  Spearman correlation test  N=0  
HISTOLOGICAL TYPE  ANOVA test  N=16  
RADIATIONS RADIATION REGIMENINDICATION  t test  N=1  yes  N=1  no  N=0 
Time to Death  Duration (Months)  0173.6 (median=21.7) 
censored  N = 187  
death  N = 13  
Significant markers  N = 0 
AGE  Mean (SD)  62.73 (11) 
Significant markers  N = 0 
HISTOLOGICAL.TYPE  Labels  N 
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA  164  
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2)  3  
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1)  3  
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3)  4  
MIXED SEROUS AND ENDOMETRIOID  3  
SEROUS ENDOMETRIAL ADENOCARCINOMA  23  
Significant markers  N = 16 
ANOVA_P  Q  

TP53P53RV  7.144e12  1.19e09 
CHEK2CHK2_PT68RC  7.824e09  1.29e06 
AKT1 AKT2 AKT3AKT_PS473RV  6.908e08  1.13e05 
PGRPRRV  1.307e07  2.13e05 
CDC2CDK1RV  2.576e07  4.17e05 
CDH1ECADHERINRV  2.644e07  4.26e05 
ESR1ERALPHARV  9.567e07  0.000153 
ESR1ERALPHA_PS118RV  3.992e06  0.000635 
EEF2EEF2RV  7.75e06  0.00122 
EIF4EBP14EBP1_PS65RV  1.874e05  0.00294 
One gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION  Labels  N 
NO  80  
YES  120  
Significant markers  N = 1  
Higher in YES  1  
Higher in NO  0 
T(pos if higher in 'YES')  ttestP  Q  AUC  

CHEK1CHK1_PS345RC  3.69  0.0002956  0.0491  0.631 

Expresson data file = UCECTP.rppa.txt

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

Number of patients = 200

Number of genes = 166

Number of clinical features = 4
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 multiclass clinical features (ordinal or nominal), oneway analysis of variance (Howell 2002) was applied to compare the log2expression levels between different clinical classes using 'anova' 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.