SNP6 Copy number analysis (GISTIC2)
View Report | There were 295 tumor samples used in this analysis: 40 significant arm-level results, 27 significant focal amplifications, and 29 significant focal deletions were found.

Correlation between aggregated molecular cancer subtypes and selected clinical features
View Report | Testing the association between subtypes identified by 10 different clustering approaches and 39 clinical features across 307 patients, 68 significant findings detected with P value < 0.05 and Q value < 0.25.

Correlation between copy number variation genes (focal events) and selected clinical features
View Report | Testing the association between copy number variation 56 focal events and 39 clinical features across 295 patients, 10 significant findings detected with Q value < 0.25.

Correlation between copy number variations of arm-level result and selected clinical features
View Report | Testing the association between copy number variation 82 arm-level events and 39 clinical features across 295 patients, 14 significant findings detected with Q value < 0.25.

Correlation between mRNAseq expression and clinical features
View Report | Testing the association between 18782 genes and 39 clinical features across 304 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 24 clinical features related to at least one genes.

Clustering of copy number data by focal peak region with absolute value: consensus NMF
View Report | The most robust consensus NMF clustering of 295 samples using the 56 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

Clustering of copy number data by peak region with threshold value: consensus NMF
View Report | The most robust consensus NMF clustering of 295 samples using the 56 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

Clustering of lincRNA expression: consensus hierarchical
View Report | Median absolute deviation (MAD) was used to select 2500 most variable lincRNAs. Consensus ward linkage hierarchical clustering of 303 samples and 2500 lincRNAs identified 7 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Clustering of lincRNA expression: consensus NMF
View Report | The most robust consensus NMF clustering of 304 samples using the 2500 most variable lincRNAs was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

Clustering of miR mature expression: consensus hierarchical
View Report | Median absolute deviation (MAD) was used to select 290 most variable miRs. Consensus ward linkage hierarchical clustering of 306 samples and 290 miRs identified 5 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Clustering of miR mature expression: consensus NMF
View Report | The most robust consensus NMF clustering of 307 samples using the 290 most variable miRs was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

Clustering of protein coding gene expression: consensus NMF
View Report | The most robust consensus NMF clustering of 304 samples using the 2500 most variable genes was identified for k = 4 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

Clustering of Protein-coding gene expression: consensus hierarchical
View Report | Median absolute deviation (MAD) was used to select 2500 most variable genes. Consensus ward linkage hierarchical clustering of 303 samples and 2500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Identification of putative miR direct targets by sequencing data
View Report | The CLR algorithm was applied on 795 miRs and 18782 mRNAs across 304 samples. After 2 filtering steps, the number of 100 miR:gene pairs were detected.

Methylation__HM450_Clustering_CNMF
View Report | The most robust consensus NMF clustering of 307 samples using the 11937 most variable genes was identified for k = 6 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

Methylation__HM450_Clustering_Consensus_Plus
View Report | Median absolute deviation (MAD) was used to select 2500 most variable genes. Consensus ward linkage hierarchical clustering of 306 samples and 2500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Correlation between copy number variation genes (focal events) and molecular subtypes
View Report | Testing the association between copy number variation 56 focal events and 10 molecular subtypes across 295 patients, 274 significant findings detected with P value < 0.05 and Q value < 0.25.

Correlation between copy number variations of arm-level result and molecular subtypes
View Report | Testing the association between copy number variation 82 arm-level events and 10 molecular subtypes across 295 patients, 258 significant findings detected with P value < 0.05 and Q value < 0.25.