SNP6 Copy number analysis (GISTIC2)
View Report | There were 568 tumor samples used in this analysis: 35 significant arm-level results, 27 significant focal amplifications, and 33 significant focal deletions were found.

Correlation between aggregated molecular cancer subtypes and selected clinical features
View Report | Testing the association between subtypes identified by 8 different clustering approaches and 8 clinical features across 579 patients, 6 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 60 focal events and 8 clinical features across 564 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 8 clinical features across 564 patients, 37 significant findings detected with Q value < 0.25.

Correlation between mRNAseq expression and clinical features
View Report | Testing the association between 19021 genes and 7 clinical features across 374 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 2 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 564 samples using the 60 most variable genes 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 copy number data by peak region with threshold value: consensus NMF
View Report | The most robust consensus NMF clustering of 564 samples using the 60 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 lincRNA expression: consensus hierarchical
View Report | Median absolute deviation (MAD) was used to select 2500 most variable lincRNAs. Consensus ward linkage hierarchical clustering of 373 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 374 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 254 most variable miRs. Consensus ward linkage hierarchical clustering of 488 samples and 254 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 489 samples using the 254 most variable miRs 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 NMF
View Report | The most robust consensus NMF clustering of 374 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 373 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 732 miRs and 19021 mRNAs across 371 samples. After 2 filtering steps, the number of 44 miR:gene pairs were detected.

Methylation__HM27_Clustering_CNMF
View Report | The most robust consensus NMF clustering of 581 samples using the 2414 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.

Correlation between copy number variation genes (focal events) and molecular subtypes
View Report | Testing the association between copy number variation 60 focal events and 8 molecular subtypes across 564 patients, 189 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 8 molecular subtypes across 564 patients, 195 significant findings detected with P value < 0.05 and Q value < 0.25.