External Resources

FireBrowse is a simple and elegant way to explore cancer data, backed by a powerful computational infrastructure, application programming interface (API), graphical tools and online reports. It sits above the TCGA GDAC Firehose, one of the deepest and most integratively characterized open cancer datasets in the world--with over 80K sample aliquots from 11,000+ cancer patients, spanning 38 unique disease cohorts. ^ref

TumorScape is designed to facilitate the use and understanding of high-resolution copy number data amassed from multiple cancer types. The functionalities, including gene-level analysis, analysis by cancer type, download and visualization of cancer DNA copy number data, are supported. ^ref

The Cancer Cell Line Encyclopedia (CCLE) project is an effort to conduct a detailed genetic characterization of a large panel of human cancer cell lines. The CCLE provides public access analysis and visualization of DNA copy number, mRNA expression, mutation data and more, for 1000 cancer cell lines. ^ref

CellMiner™ is a web application that facilitates systems biology through the retrieval and integration of the molecular and pharmacological data sets for the NCI-60 cell lines. The NCI-60 is a panel of 60 diverse human cancer cell lines used by the Developmental Therapeutics Program of the U.S. National Cancer Institute to screen over 100,000 chemical compounds and natural products (since 1990). ^ref

The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. ^ref

Oncomine combines a rapidly growing compendium of 20,000+ cancer transcriptome profiles with a sophisticated analysis engine and a powerful web application for data-mining and visualization. ^ref

The UCSC Cancer Browser allows researchers to interactively explore cancer genomics data and its associated clinical information. Data can be viewed in a variety of ways, including by value, chromosome location, clinical feature, biological pathway or geneset of interest. It is also possible to quickly perform and easily view statistical analyses on subsets of the data. ^ref

Genome-scale Integrated Analysis of gene Networks in Tissues (GIANT) provides an interface to human tissue networks through multi-gene queries, network visualization, analysis tools (including NetWAS) and downloadable networks. GIANT enables systematic exploration of the landscape of interacting genes that shape specialized cellular functions across more than a hundred human tissues and cell types. ^ref

The Expression Atlas provides information on gene expression patterns under different biological conditions. Gene expression data is re-analyzed in-house to detect genes showing interesting baseline and differential expression patterns. ^ref

BioGPS is an extensible and customizable portal for querying and organizing gene annotation resources. In particular, its default gene annotation report provides a survey of gene expression patterns from a diverse set of tissues and cell types. ^ref

Enrichr is an easy-to-use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists. Enrichr provides access to 35 gene-set libraries with many useful libraries such as those created from ENCODE enlisting many targets for many transcription factors as well as a gene-set library extracted from the NIH Roadmap Epigenomics Project for histone modifications. ^ref

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind a large list of genes. ^ref

GOrilla (Gene Ontology enRIchment anaLysis and visuaLizAtion tool) is a tool for discovery and visualization of enriched GO terms in ranked gene lists ^ref

Please let me know: Email any additional resources to ling[dot]cai[at]utsouthwestern[dot]edu