(primary solid tumor cohort)
This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18257 genes and 4 clinical features across 153 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.

1 gene correlated to 'AGE'.

ADAP255803

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

C14ORF126112487 , CEBPZ10153 , ABHD1183451 , SFRS26427 , MCOLN2255231 , ...

1 gene correlated to 'COMPLETENESS.OF.RESECTION'.

GLP2R9340

No genes correlated to 'NUMBER.OF.LYMPH.NODES'
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=1  younger  N=0 
RADIATIONS RADIATION REGIMENINDICATION  t test  N=30  yes  N=8  no  N=22 
COMPLETENESS OF RESECTION  ANOVA test  N=1  
NUMBER OF LYMPH NODES  Spearman correlation test  N=0 
AGE  Mean (SD)  60.49 (6.9) 
Significant markers  N = 1  
pos. correlated  1  
neg. correlated  0 
SpearmanCorr  corrP  Q  

ADAP255803  0.388  7.87e07  0.0144 
30 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION  Labels  N 
NO  5  
YES  148  
Significant markers  N = 30  
Higher in YES  8  
Higher in NO  22 
T(pos if higher in 'YES')  ttestP  Q  AUC  

C14ORF126112487  10.72  3.125e17  5.47e13  0.8527 
CEBPZ10153  10.55  2.889e16  5.05e12  0.8554 
ABHD1183451  12.03  4.211e12  7.37e08  0.9108 
SFRS26427  10.08  3.636e11  6.36e07  0.8392 
MCOLN2255231  7.14  1.947e10  3.41e06  0.7054 
CDC4051362  9.28  3.636e10  6.36e06  0.8514 
TMEM161B153396  8.76  2.362e09  4.13e05  0.8851 
SFRS13A10772  9.78  3.218e09  5.63e05  0.873 
ABCD1215  8.33  3.263e09  5.71e05  0.8122 
PPIG9360  7.15  4.42e09  7.73e05  0.7095 
COMPLETENESS.OF.RESECTION  Labels  N 
R0  117  
R1  29  
RX  2  
Significant markers  N = 1 
ANOVA_P  Q  

GLP2R9340  9.218e10  1.68e05 

Expresson data file = PRADTP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

Number of patients = 153

Number of genes = 18257

Number of clinical features = 4
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 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 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.