Analysis of mutagenesis by APOBEC cytidine deaminases (P-MACD).
View Report | There are 796 tumor samples in this analysis. The Benjamini-Hochberg-corrected p-value for enrichment of the APOBEC mutation signature in 1 samples is <=0.05. Out of these, 1 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).

CHASM 1.0.5 (Cancer-Specific High-throughput Annotation of Somatic Mutations)
View Report | There are 36580 mutations identified by MuTect and 2635 mutations with significant functional impact at BHFDR <= 0.25.

LowPass Copy number analysis (GISTIC2)
View Report | There were 52 tumor samples used in this analysis: 12 significant arm-level results, 3 significant focal amplifications, and 2 significant focal deletions were found.

Mutation Analysis (MutSig 2CV v3.1)
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Mutation Analysis (MutSig v2.0)
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Mutation Analysis (MutSigCV v0.9)
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Mutation Assessor
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SNP6 Copy number analysis (GISTIC2)
View Report | There were 1090 tumor samples used in this analysis: 27 significant arm-level results, 32 significant focal amplifications, and 47 significant focal deletions were found.

Correlation between aggregated molecular cancer subtypes and selected clinical features
View Report | Testing the association between subtypes identified by 14 different clustering approaches and 9 clinical features across 1107 patients, 61 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 79 focal events and 9 clinical features across 1083 patients, 418 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 9 clinical features across 1083 patients, 359 significant findings detected with Q value < 0.25.

Correlation between gene methylation status and clinical features
View Report | Testing the association between 20122 genes and 9 clinical features across 651 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 8 clinical features related to at least one genes.

Correlation between gene mutation status and selected clinical features
View Report | Testing the association between mutation status of 174 genes and 9 clinical features across 790 patients, 91 significant findings detected with Q value < 0.25.

Correlation between miR expression and clinical features
View Report | Testing the association between 534 miRs and 8 clinical features across 561 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 5 clinical features related to at least one miRs.

Correlation between miRseq expression and clinical features
View Report | Testing the association between 548 miRs and 8 clinical features across 511 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 7 clinical features related to at least one miRs.

Correlation between mRNA expression and clinical features
View Report | Testing the association between 12042 genes and 8 clinical features across 525 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 6 clinical features related to at least one genes.

Correlation between mRNAseq expression and clinical features
View Report | Testing the association between 18325 genes and 9 clinical features across 667 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 10 clinical features across 790 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 6 clinical features related to at least one variables.

Correlation between RPPA expression and clinical features
View Report | Testing the association between 217 genes and 9 clinical features across 658 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 8 clinical features related to at least one genes.

Clustering of copy number data by focal peak region with log2 ratio: consensus NMF
View Report | The most robust consensus NMF clustering of 1090 samples using the 79 copy number focal regions 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 copy number data by peak region with threshold value: consensus NMF
View Report | The most robust consensus NMF clustering of 1090 samples using the 79 copy number focal regions was identified for k = 7 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

Clustering of Methylation: consensus NMF
View Report | The 8117 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 656 samples and 8117 genes 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 | Median absolute deviation (MAD) was used to select 133 most variable miRs. Consensus ward linkage hierarchical clustering of 565 samples and 133 miRs identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Clustering of miR expression: consensus NMF
View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 565 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 miRseq mature expression: consensus hierarchical
View Report | Median absolute deviation (MAD) was used to select 647 most variable miRs. Consensus ward linkage hierarchical clustering of 508 samples and 647 miRs identified 4 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Clustering of miRseq mature expression: consensus NMF
View Report | We filtered the data to 647 most variable miRs. Consensus NMF clustering of 508 samples and 647 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.

Clustering of miRseq precursor expression: consensus hierarchical
View Report | Median absolute deviation (MAD) was used to select 137 most variable miRs. Consensus ward linkage hierarchical clustering of 512 samples and 137 miRs identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Clustering of miRseq precursor expression: consensus NMF
View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 512 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 mRNA expression: consensus hierarchical
View Report | Median absolute deviation (MAD) was used to select 1500 most variable genes. Consensus ward linkage hierarchical clustering of 528 samples and 1500 genes identified 4 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Clustering of mRNA expression: consensus NMF
View Report | The most robust consensus NMF clustering of 528 samples using the 1500 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 to determine the best solution.

Clustering of mRNAseq gene expression: consensus hierarchical
View Report | Median absolute deviation (MAD) was used to select 1500 most variable genes. Consensus ward linkage hierarchical clustering of 669 samples and 1500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Clustering of mRNAseq gene expression: consensus NMF
View Report | The most robust consensus NMF clustering of 669 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 RPPA data: consensus hierarchical
View Report | Median absolute deviation (MAD) was used to select 213 most variable proteins. Consensus ward linkage hierarchical clustering of 662 samples and 213 proteins identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Clustering of RPPA data: consensus NMF
View Report | The most robust consensus NMF clustering of 662 samples using 213 proteins 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.

Aggregate Analysis Features
View Report | 1115 samples and 958 features are included in this feature table. The figures below show which genomic pair events are co-occurring and which are mutually-exclusive.

Identification of putative miR direct targets by microarray data
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.

Identification of putative miR direct targets by sequencing data
View Report | The CLR algorithm was applied on 776 miRs and 18325 mRNAs across 512 samples. After 2 filtering steps, the number of 84 miR:genes pairs were detected.

Association of mutation, copy number alteration, and subtype markers with pathways
View Report | There are 130 genes with significant mutation (Q value <= 0.1) and 163 genes with significant copy number alteration (Q value <= 0.25). The identified marker genes (Q value <= 0.01 or within top 2000) are 1738 for subtype 1, 1738 for subtype 2, 1738 for subtype 3. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in GBMLGG-TP
View Report | basic data info

PARADIGM pathway analysis of mRNA expression and copy number data
View Report | There were 82 significant pathways identified in this analysis.

PARADIGM pathway analysis of mRNA expression data
View Report | There were 47 significant pathways identified in this analysis.

PARADIGM pathway analysis of mRNASeq expression and copy number data
View Report | There were 61 significant pathways identified in this analysis.

PARADIGM pathway analysis of mRNASeq expression data
View Report | There were 64 significant pathways identified in this analysis.

Significant over-representation of pathway genesets for a given gene list
View Report | For a given gene list, a hypergeometric test was tried to find significant overlapping canonical pathway gene sets. In terms of FDR adjusted p.values, top 5 significant overlapping gene sets are listed as below.

Correlation between copy number and miR expression
View Report

Correlation between copy number variation genes (focal events) and molecular subtypes
View Report | Testing the association between copy number variation 79 focal events and 14 molecular subtypes across 1090 patients, 667 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 14 molecular subtypes across 1090 patients, 549 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 174 genes and 14 molecular subtypes across 796 patients, 194 significant findings detected with P value < 0.05 and Q value < 0.25.

Correlation between mRNA expression and DNA methylation
View Report | The top 25 correlated methylation probes per gene are displayed. Total number of matched samples = 567. Number of gene expression samples = 669. Number of methylation samples = 656.

Correlations between copy number and mRNA expression
View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are -0.0123, 0.02434, 0.0601, 0.09808, 0.1379, 0.17972, 0.2216, 0.2685, 0.3379, respectively.

Correlations between copy number and mRNAseq expression
View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 829.5, 1618, 2081, 2530, 3021, 3549, 4161, 4829, 5694.5, respectively.