This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18254 genes and 4 clinical features across 834 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.

4 genes correlated to 'Time to Death'.

DIP2B57609 , PGK15230 , CAND155832 , IRF23660

689 genes correlated to 'AGE'.

ESR12099 , TFPI27980 , LRFN5145581 , TMEFF18577 , SOBP55084 , ...

18 genes correlated to 'GENDER'.

NLGN4Y22829 , ZFY7544 , PRKY5616 , C7ORF1079783 , SYT9143425 , ...

No genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'
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=4  shorter survival  N=3  longer survival  N=1 
AGE  Spearman correlation test  N=689  older  N=163  younger  N=526 
GENDER  t test  N=18  male  N=8  female  N=10 
RADIATIONS RADIATION REGIMENINDICATION  t test  N=0 
Time to Death  Duration (Months)  0223.4 (median=18.9) 
censored  N = 683  
death  N = 94  
Significant markers  N = 4  
associated with shorter survival  3  
associated with longer survival  1 
HazardRatio  Wald_P  Q  C_index  

DIP2B57609  2.9  1.611e07  0.0029  0.635 
PGK15230  2  1.673e06  0.031  0.685 
CAND155832  2.1  1.686e06  0.031  0.629 
IRF23660  0.28  1.983e06  0.036  0.329 
AGE  Mean (SD)  58.18 (13) 
Significant markers  N = 689  
pos. correlated  163  
neg. correlated  526 
SpearmanCorr  corrP  Q  

ESR12099  0.3524  9.285e26  1.69e21 
TFPI27980  0.268  4.569e15  8.34e11 
LRFN5145581  0.2692  5.372e15  9.81e11 
TMEFF18577  0.2528  1.31e13  2.39e09 
SOBP55084  0.2517  1.69e13  3.08e09 
DBX2440097  0.2673  4.243e13  7.74e09 
DZIP122873  0.2461  5.847e13  1.07e08 
PCDH1854510  0.2459  6.176e13  1.13e08 
RELN5649  0.2468  9.321e13  1.7e08 
FXYD653826  0.2409  1.831e12  3.34e08 
GENDER  Labels  N 
FEMALE  825  
MALE  9  
Significant markers  N = 18  
Higher in MALE  8  
Higher in FEMALE  10 
T(pos if higher in 'MALE')  ttestP  Q  AUC  

NLGN4Y22829  41.17  2.294e12  4.12e08  1 
ZFY7544  41.94  1.786e11  3.21e07  1 
PRKY5616  27.63  6.061e10  1.09e05  1 
C7ORF1079783  8.61  3.928e09  7.06e05  0.6626 
SYT9143425  12.51  5.949e09  0.000107  0.7954 
GSTA12938  16.04  8.563e09  0.000154  0.8829 
MMP114320  11.05  1.626e08  0.000292  0.7461 
RND28153  12.35  2.543e08  0.000457  0.8361 
SNORA74B677841  12  8.287e08  0.00149  0.8348 
HTR43360  12.07  1.118e07  0.00201  0.7909 

Expresson data file = BRCATP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

Number of patients = 834

Number of genes = 18254

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 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.