This pipeline uses various statistical tests to identify RPPAs whose expression levels correlated to selected clinical features.
Testing the association between 165 genes and 5 clinical features across 407 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.

2 genes correlated to 'Time to Death'.

MAPK1 MAPK3MAPK_PT202_Y204RV , MAP2K1MEK1_PS217_S221RV

4 genes correlated to 'AGE'.

PGRPRRV , ESR1ERALPHARV , ERBB2HER2MV , ERBB2HER2_PY1248RV

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

METCMETMC

No genes correlated to 'PRIMARY.SITE.OF.DISEASE', 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=2  shorter survival  N=2  longer survival  N=0 
AGE  Spearman correlation test  N=4  older  N=3  younger  N=1 
PRIMARY SITE OF DISEASE  ANOVA test  N=0  
KARNOFSKY PERFORMANCE SCORE  Spearman correlation test  N=0  
COMPLETENESS OF RESECTION  ANOVA test  N=1 
Time to Death  Duration (Months)  0.3180.2 (median=28.5) 
censored  N = 189  
death  N = 212  
Significant markers  N = 2  
associated with shorter survival  2  
associated with longer survival  0 
HazardRatio  Wald_P  Q  C_index  

MAPK1 MAPK3MAPK_PT202_Y204RV  1.27  0.0001224  0.02  0.574 
MAP2K1MEK1_PS217_S221RV  1.9  0.0001462  0.024  0.58 
AGE  Mean (SD)  59.67 (12) 
Significant markers  N = 4  
pos. correlated  3  
neg. correlated  1 
SpearmanCorr  corrP  Q  

PGRPRRV  0.1954  8.394e05  0.0139 
ESR1ERALPHARV  0.1902  0.0001296  0.0213 
ERBB2HER2MV  0.1876  0.0001607  0.0262 
ERBB2HER2_PY1248RV  0.1816  0.0002611  0.0423 
PRIMARY.SITE.OF.DISEASE  Labels  N 
OMENTUM  2  
OVARY  403  
PERITONEUM OVARY  2  
Significant markers  N = 0 
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE  Mean (SD)  74.9 (12) 
Score  N  
40  1  
60  14  
80  33  
100  3  
Significant markers  N = 0 
COMPLETENESS.OF.RESECTION  Labels  N 
R0  13  
R1  28  
R2  2  
Significant markers  N = 1 
ANOVA_P  Q  

METCMETMC  9.338e05  0.0154 

Expresson data file = OVTP.rppa.txt

Clinical data file = OVTP.merged_data.txt

Number of patients = 407

Number of genes = 165

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 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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.