SNP6 Copy number analysis (GISTIC2)
View Report | There were 517 tumor samples used in this analysis: 36 significant arm-level results, 24 significant focal amplifications, and 37 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 14 clinical features across 528 patients, 48 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 61 focal events and 14 clinical features across 517 patients, 50 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 14 clinical features across 517 patients, one significant finding detected with Q value < 0.25.

Clustering of copy number data by focal peak region with absolute value: consensus NMF
View Report | The most robust consensus NMF clustering of 517 samples using the 61 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 517 samples using the 61 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.

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 499 samples and 2500 lincRNAs identified 3 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 500 samples using the 2500 most variable lincRNAs was identified for k = 5 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 299 most variable miRs. Consensus ward linkage hierarchical clustering of 522 samples and 299 miRs identified 3 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 523 samples using the 299 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 500 samples using the 2500 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 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 499 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 793 miRs and 18910 mRNAs across 495 samples. After 2 filtering steps, the number of 162 miR:gene pairs were detected.

Methylation__HM450_Clustering_CNMF
View Report | The most robust consensus NMF clustering of 527 samples using the 5595 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.

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 526 samples and 2500 genes identified 7 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 61 focal events and 10 molecular subtypes across 517 patients, 429 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 517 patients, 450 significant findings detected with P value < 0.05 and Q value < 0.25.