Analysis of mutagenesis by APOBEC cytidine deaminases (P-MACD).
View Report | There are 100 tumor samples in this analysis. The Benjamini-Hochberg-corrected p-value for enrichment of the APOBEC mutation signature in 0 samples is <=0.05. Out of these, 0 have enrichment values >2, which implies that in such samples at least 50% of APOBEC signature mutations have been in fact made by APOBEC enzyme(s).

Mutation Analysis (MutSig 2CV v3.1)
View Report | 

Mutation Signature Analysis
View Report | Our analysis idenfied 3 solution(s) of mutational signatures across 100 samples by BayesNMF method.

SNP6 Copy number analysis (GISTIC2)
View Report | There were 100 tumor samples used in this analysis: 41 significant arm-level results, 48 significant focal amplifications, and 63 significant focal deletions were found.

Correlation between aggregated molecular cancer subtypes and selected clinical features
View Report | Testing the association between subtypes identified by 3 different clustering approaches and 17 clinical features across 100 patients, 3 significant findings detected with P value < 0.05 and Q value < 0.25.

Correlation between APOBEC signature variables and clinical features
View Report | Testing the association between 3 variables and 17 clinical features across 100 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 4 clinical features related to at least one variables.

Correlation between copy number variation genes (focal events) and selected clinical features
View Report | Testing the association between copy number variation 110 focal events and 17 clinical features across 100 patients, 98 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 72 arm-level events and 17 clinical features across 100 patients, 76 significant findings detected with Q value < 0.25.

Correlation between gene mutation status and selected clinical features
View Report | Testing the association between mutation status of 388 genes and 17 clinical features across 100 patients, no significant finding detected with Q value < 0.25.

Correlation between mRNAseq expression and clinical features
View Report | Testing the association between 18424 genes and 17 clinical features across 100 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 8 clinical features related to at least one genes.

Correlation between mutation rate and clinical features
View Report | Testing the association between 2 variables and 18 clinical features across 100 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 1 clinical feature related to at least one variables.

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 100 samples and 2500 genes identified 5 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Aggregate_Analysis_Features
View Report | 99 samples and 1161 features are included in this feature table. The figures below show which genomic pair events are co-occurring and which are mutually-exclusive.

Methylation__EPIC_Clustering_CNMF
View Report | The most robust consensus NMF clustering of 96 samples using the 6355 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 and the average silhouette width calculation to determine the robust clusters.

Methylation__EPIC_Clustering_Consensus_Plus
View Report | Median absolute deviation (MAD) was used to select 2500 most variable genes. Consensus ward linkage hierarchical clustering of 96 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 110 focal events and 3 molecular subtypes across 100 patients, 97 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 72 arm-level events and 3 molecular subtypes across 100 patients, 67 significant findings detected with P value < 0.05 and Q value < 0.25.

Correlation between gene mutation status and molecular subtypes
View Report | Testing the association between mutation status of 388 genes and 3 molecular subtypes across 100 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.