Pathway analysis of genetic alterations in glioblastoma (TCGA)

Mondrian, the Genome Data Mapper Software, maps genomic data onto pathways.

To map genomic data from the glioblastoma project onto a pathway of genes frequently altered in glioblastoma, use one of the buttons below:

Visualize GBM data in the context of pathways using Mondrian
91 Sample Dataset 206 Sample Dataset
copy number, mRNA expression, mutations copy number, mRNA expression

Using information from the literature and public pathway databases, we have assembled a pathway representation of the most frequently altered genes in glioblastoma. This pathway is available as a Cytoscape session file or as a PDF document.
GBM pathway representation (PDF and Cytoscape)

In collaboration with Lawrence Donehower, David Wheeler and Beatriz Santillan at Baylor College of Medicine, we have analyzed alterations of individual sub-pathways using copy-number alterations and mutations in 601 genes. Results from this analysis are part of the TCGA consortium paper, and can also be viewed here:
Frequency of alterations mapped onto signaling pathways
Sample-by-sample view of alterations

- Copy-number alterations and mutations of pathway genes (91 samples)
       - per sample spreadsheet (PDF)
       - overall percentages mapped onto the GBM pathway (PDF)

- Copy-number alterations mapped on the GBM pathway (206 samples)
       - per sample spreadsheet (PDF)
       - overall percentages mapped onto the GBM pathway (PDF)

Data Portal

Access TCGA genomic data via our Data Portal.

Gene Ranker

Explore TCGA Phase III sequencing genes with Gene Ranker.

News

The Cancer Genome Atlas Reports First Results Of Comprehensive Study of Brain Tumors (4 September 2008, NIH Press Release)

Cancer complexity slows quest for cure (4 September 2008, Nature)

An Integrated Genomic Analysis of Human Glioblastoma Multiforme. D. Williams Parsons, et. al. (4 September, Science)

Publications

Comprehensive genomic characterization defines human glioblastoma genes and core pathways. The Cancer Genome Atlas Research Network. (4 September 2008, Nature) [Abstract] [PDF] [Supplementary information]

CancerGenes: a gene selection resource for cancer genome projects. Higgins ME, et. al. Nucleic Acids Res. 2007 Jan (Database issue:D721-6. [PubMed Abstract] [Full Text] [PDF]