The candidate gene list for the sarcoma sequencing effort was compiled from a variety of curated lists, cancer and sarcoma reviews, and Entrez Gene queries, followed by a additional curation (in progress). The resulting gene list includes the gene symbol, gene name, description, chromosome, location, Entrez GeneID, Entrez HyperLink, COSMIC Hyperlink, gene ontology (GO) terms, InterPro Descriptions, and data source.
The cBio Cancer Genomics Data Portal provides direct download and visualization of large-scale cancer genomics data sets. It currently provides direct access to the TCGA data sets for the Glioblastoma Multiforme (GBM) pilot-project.
The Mondrian Software enables researchers to visualize complex multi-dimensional genomic profiling data in the context of known biological pathways.
NetBox is a Java-based software tool for performing network analysis on human interaction networks. It is pre-loaded with a Human Interaction Network (HIN) derived from four literature curated data sources, including the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway Interaction (PID) Database, and the MSKCC Cancer Cell Map.
Currently, NetBox provides the analyzeNet.py method that is fully described in the manuscript: Automated Network Analysis Identifies Core Pathways in Glioblastoma (Currently in Review). This provides a simple command line interface for connecting genes into a network, identifying statistically significant "linker" genes, partitioning the network into modules, and executing two random background models. Results are then made available to the end user as an HTML web page and a series of network and attribute files, which can be loaded into Cytoscape for visualization and further analysis.
