Copy number analysis (GISTIC2)
View Report | There were 413 tumor samples used in this analysis: 23 significant arm-level results, 24 significant focal amplifications, and 44 significant focal deletions were found.

Mutation Analysis (MutSig)
View Report | 

Mutation Analysis (MutSig)
View Report | 

Clustering of copy number data: consensus NMF
View Report | The most robust consensus NMF clustering of 413 samples using the 68 copy number focal regions was identified for k = 4 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

Clustering of Methylation: consensus NMF
View Report | The 6793 most variable methylated genes were selected based on variation. The variation cutoff are set for each tumor type empirically by fitting a bimodal distriution. For genes with multiple methylation probes, we chose the most variable one to represent the gene. Consensus NMF clustering of 254 samples and 6793 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

Clustering of RPPA data: consensus NMF
View Report | The most robust consensus NMF clustering of 269 samples using the 150 most variable proteins was identified for k = 4 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

Clustering of RPPA data: consensus hierarchical
View Report | The 150 most variable proteins were selected. Consensus average linkage hierarchical clustering of 269 samples and 150 proteins identified 4 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

Clustering of mRNA expression: consensus NMF
View Report | The most robust consensus NMF clustering of 155 samples using the 1500 most variable genes was identified for k = 4 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

Clustering of mRNA expression: consensus hierarchical
View Report | The 1500 most variable genes were selected. Consensus average linkage hierarchical clustering of 155 samples and 1500 genes identified 4 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

Clustering of miRseq expression: consensus NMF
View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 378 samples and 150 miRs identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

Clustering of miRseq expression: consensus hierarchical
View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 378 samples and 150 miRs identified 4 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

Correlation between copy number variations of arm-level result and selected clinical features
View Report | Testing the association between copy number variation 76 arm-level results and 10 clinical features across 413 patients, 18 significant findings detected with Q value < 0.25.

Correlation between copy number variation genes and selected clinical features
View Report | Testing the association between copy number variation of 68 peak regions and 10 clinical features across 413 patients, 34 significant findings detected with Q value < 0.25.

Correlation between molecular cancer subtypes and selected clinical features
View Report | Testing the association between subtypes identified by 8 different clustering approaches and 10 clinical features across 422 patients, 20 significant findings detected with P value < 0.05.

Correlation between gene mutation status and selected clinical features
View Report | Testing the association between mutation status of 181 genes and 9 clinical features across 155 patients, 3 significant findings detected with Q value < 0.25.

Correlation between RPPA expression and clinical features
View Report | Testing the association between 171 genes and 10 clinical features across 269 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.

Correlation between mRNA expression and clinical features
View Report | Testing the association between 17814 genes and 9 clinical features across 155 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.

Correlation between miRseq expression and clinical features
View Report | Testing the association between 415 genes and 9 clinical features across 378 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.

Correlations between copy number and mRNA expression
View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are -0.0474, 0.0154, 0.0723, 0.1326, 0.2034, 0.2758, 0.3497, 0.4281, 0.5197, respectively.

Association of mutation, copy number alteration, and subtype markers with pathways
View Report | There are 87 genes with significant mutation (Q value <= 0.1) and 328 genes with significant copy number alteration (Q value <= 0.25). The identified marker genes (Q value <= 0.01 or within top 2000) are 2000 for subtype 1, 2000 for subtype 2, 2000 for subtype 3, 2000 for subtype 4. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

PARADIGM pathway analysis of mRNA expression data
View Report | There were 57 significant pathways identified in this analysis.

PARADIGM pathway analysis of mRNA expression and copy number data
View Report | There were 53 significant pathways identified in this analysis.