This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18155 genes and 3 clinical features across 53 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.

1 gene correlated to 'AGE'.

OSBPL9114883

10 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

SCN11A11280 , TSPAN19144448 , ZNF596169270 , SFRS26427 , VN1R157191 , ...

77 genes correlated to 'NEOADJUVANT.THERAPY'.

KIAA164485352 , SPOCK350859 , PDPN10630 , HSPB826353 , DCBLD2131566 , ...
Complete statistical result table is provided in Supplement Table 1
Clinical feature  Statistical test  Significant genes  Associated with  Associated with  

AGE  Spearman correlation test  N=1  older  N=0  younger  N=1 
RADIATIONS RADIATION REGIMENINDICATION  t test  N=10  yes  N=3  no  N=7 
NEOADJUVANT THERAPY  t test  N=77  yes  N=59  no  N=18 
AGE  Mean (SD)  61.3 (7.2) 
Significant markers  N = 1  
pos. correlated  0  
neg. correlated  1 
SpearmanCorr  corrP  Q  

OSBPL9114883  0.6211  6.951e07  0.0126 
10 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION  Labels  N 
NO  4  
YES  49  
Significant markers  N = 10  
Higher in YES  3  
Higher in NO  7 
T(pos if higher in 'YES')  ttestP  Q  AUC  

SCN11A11280  8.92  7.261e08  0.00125  0.9583 
TSPAN19144448  7.97  1.119e07  0.00192  0.907 
ZNF596169270  7.67  2.379e07  0.00408  0.9235 
SFRS26427  6.38  3.135e07  0.00538  0.8367 
VN1R157191  6.13  3.556e07  0.0061  0.8724 
UBTF7343  6.6  4.129e07  0.00709  0.8724 
FGFR32261  5.46  1.407e06  0.0241  0.7806 
C15ORF5790416  5.56  1.485e06  0.0255  0.7908 
ELP355140  5.36  2.3e06  0.0395  0.7347 
ABHD1183451  5.76  2.676e06  0.0459  0.852 
NEOADJUVANT.THERAPY  Labels  N 
NO  3  
YES  50  
Significant markers  N = 77  
Higher in YES  59  
Higher in NO  18 
T(pos if higher in 'YES')  ttestP  Q  AUC  

KIAA164485352  15.32  2.098e17  3.38e13  1 
SPOCK350859  14.03  2.622e17  4.22e13  0.9867 
PDPN10630  13.08  1.503e16  2.42e12  0.9467 
HSPB826353  16.25  1.626e16  2.62e12  1 
DCBLD2131566  11.25  2.2e15  3.54e11  0.94 
PTPN95780  11.21  3.201e15  5.15e11  0.9467 
TGFB1I17041  13.78  1.156e13  1.86e09  0.98 
FGFR12260  9.95  2.136e13  3.44e09  0.92 
ACSL623305  9.85  2.709e13  4.36e09  0.9867 
FAM13C220965  11.14  7.037e13  1.13e08  0.96 

Expresson data file = PRAD.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

Number of patients = 53

Number of genes = 18155

Number of clinical features = 3
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.