Copy number analysis (GISTIC2)
View Report | There were 560 tumor samples used in this analysis: 22 significant arm-level results, 17 significant focal amplifications, and 40 significant focal deletions were found.

Mutation Analysis (MutSig)
View Report | Significantly mutated genes (q ≤ 0.1): 223

Clustering of Methylation: consensus NMF
View Report | The 1139 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 287 samples and 1139 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 214 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 214 samples and 150 proteins 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 mRNA expression: consensus NMF
View Report | The most robust consensus NMF clustering of 529 samples using the 1500 most variable genes was identified for k = 3 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 529 samples and 1500 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 miR expression: consensus NMF
View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 491 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.

Clustering of miR expression: consensus hierarchical
View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 491 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.

Correlation between molecular cancer subtypes and selected clinical features
View Report | Testing the association between subtypes identified by 5 different clustering approaches and 7 clinical features across 527 patients, 7 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 295 genes and 7 clinical features across 269 patients, 34 significant findings detected with Q value < 0.25.

Correlation between mRNA expression and clinical features
View Report | Testing the association between 12042 genes and 7 clinical features across 519 samples, statistically thresholded by Q value < 0.05, 6 clinical features related to at least one genes.

Correlation between miR expression and clinical features
View Report | Testing the association between 534 miRs and 7 clinical features across 482 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one miRs.

Correlations between copy number and mRNA expression
View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are -0.02489, 0.0139, 0.0539, 0.10018, 0.1516, 0.20166, 0.24904, 0.3002, 0.37139, respectively.

Correlations between copy number and miR expression
View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are -0.0506, -0.02018, 0.0051, 0.01916, 0.04545, 0.08442, 0.13033, 0.21002, 0.27177, respectively.

Correlation between mRNA expression and DNA methylation
View Report | The top 25 correlated methylation probe(s) per gene are displayed. Total number of matched samples = 279 Number of gene expression samples = 289 Number of methylation samples = 529

Association of mutation, copy number alteration, and subtype markers with pathways
View Report | There are 184 genes with significant mutation (Q value <= 0.1) and 110 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. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

PARADIGM pathway analysis of mRNA expression data
View Report | There were 67 significant pathways identified in this analysis.

PARADIGM pathway analysis of mRNA expression and copy number data
View Report | There were 98 significant pathways identified in this analysis.

Identification of putative miR direct targets
View Report | This pipeline use a relevance network approach to infer putative miR:mRNA regulatory connections. All miR:mRNA pairs that have correlations < -0.3 and have predicted interactions in three sequence prediction databases (Miranda, Pictar, Targetscan) define the final network.