This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18190 genes and 5 clinical features across 152 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.

27 genes correlated to 'GENDER'.

XIST7503 , RPS4Y16192 , DDX3Y8653 , KDM5D8284 , USP9Y8287 , ...

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

ZBTB3310009

No genes correlated to 'Time to Death', 'AGE', and 'KARNOFSKY.PERFORMANCE.SCORE'.
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  
GENDER  t test  N=27  male  N=15  female  N=12 
KARNOFSKY PERFORMANCE SCORE  Spearman correlation test  N=0  
RADIATIONS RADIATION REGIMENINDICATION  t test  N=1  yes  N=0  no  N=1 
Time to Death  Duration (Months)  0.254 (median=8.7) 
censored  N = 53  
death  N = 99  
Significant markers  N = 0 
AGE  Mean (SD)  60.09 (13) 
Significant markers  N = 0 
GENDER  Labels  N 
FEMALE  54  
MALE  98  
Significant markers  N = 27  
Higher in MALE  15  
Higher in FEMALE  12 
T(pos if higher in 'MALE')  ttestP  Q  AUC  

XIST7503  37.31  2.389e54  4.34e50  1 
RPS4Y16192  48.24  2.441e54  4.44e50  1 
DDX3Y8653  49.54  3.219e49  5.85e45  1 
KDM5D8284  44.37  1.096e48  1.99e44  1 
USP9Y8287  49.48  2.069e47  3.76e43  1 
CYORF15A246126  42.68  6.12e44  1.11e39  1 
ZFY7544  49.63  9.035e42  1.64e37  1 
EIF1AY9086  42.09  2.671e41  4.85e37  1 
TSIX9383  22.15  3.036e41  5.52e37  0.9974 
PRKY5616  25.73  2.98e35  5.42e31  0.9989 
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE  Mean (SD)  75.61 (14) 
Significant markers  N = 0 
One gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION  Labels  N 
NO  97  
YES  55  
Significant markers  N = 1  
Higher in YES  0  
Higher in NO  1 
T(pos if higher in 'YES')  ttestP  Q  AUC  

ZBTB3310009  5.27  6.447e07  0.0117  0.7327 

Expresson data file = GBMTP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

Number of patients = 152

Number of genes = 18190

Number of clinical features = 5
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.