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Cancer Genomics Resources

A collection of online resources that are useful for cancer genomics. Some of these are highly specific to cancer research, while others are more general purpose, but still pertinent. The sites are broadly categorized into comprehensive repositories, sequence mutations and polymorphisms, mutation impact, gene expression, gene functions, and drug responses.

This list is not exhaustive. If your favorite online resource is not present, please let us know and we will add it to the list.

Contents

Comprehensive Cancer Genomics

  • cBioPortal is a general database and repository for genes associated with cancer. It provides visualization, analysis, and download of large-scale cancer genomics data. Data sets includes mutation, copy number, expression, and DNA methylation collected from various published sources. It is developed and maintained by the Memorial Sloan Kettering Cancer Center.
  • The Cancer Genome Atlas is an NCI project that is cataloguing and characterizing properties of a wide variety of cancers, including gene expression and sequence mutants.
  • Oncotator is an online tool and repository for annotating sequence mutations, including point mutations and indels, associated with cancer. Annotations are collected from a variety of other online resources. It is maintained by the Broad Institute.
  • Oncomine is a comprehensive resource for profiling gene expression, sequence analysis, pathways, and drug responses for a variety of different cancers. A free academic version is available, as well as a paid commercial product with more tools and functions.

Mutations

  • Cosmic is an online repository of somatic mutations found in cancers. The mutations may be searched and/or browsed by genomic location, gene, or cancer type. Mutations are collected from primary literature. In addition to sequence variants, copy number, gene fustions, and structural rearrangements are also included.
  • dbSNP is an online database of known sequence variants, including single nucleotide polymorphisms, small insertions and deletions, microsatellite variants, and non-polymorphic variants.
  • DECIPHER is an online database of submicroscopic chromosomal imbalances (deletions or duplications) identified in patients with developmental disorders.

Mutation Impact

  • PolyPhen is an online and standalone software tool that predicts the impact of missense amino acid substitutions based on known structural and evolutionary data. A number of known missense changes have already been predicted. It is limited to single nucleotide changes.
  • Mutation Taster is an online only tool for predicting the impact of sequence variants on genes, transcripts, and/or protein coding potential. A variety of sequence variants can be provided, including single- or multiple-base changes as well as short insertion/deletions.
  • Mutation Assessor is an online tool for predicting the impact of missense mutations in proteins identified in cancer and other diseases.

Gene Expression Analysis

  • Kaplan-Meier Plotter is an online tool for assessing risk in patients by comparing gene expression data associated with different patient survival outcomes. Three types of cancer are supported: breast, ovarian, and lung.
  • Gene Set Enrichment Analysis (GSEA) provides an analytical method for correlating the transcription profiles between two or more biological states, e.g. tumor and normal. Software is available for download to perform the comparisons. These in turn can be compared to an online database of gene expression signatures (Molecular Signature Database, or MSigDB).

Gene Functions

  • GeneMANIA is an online tool for associating one or more genes of interest with various functions based on protein and genetic interactions, pathways, co-expression, co-localization, and protein domain similarity.
  • DAVID is an online database for identifying biological functions, pathways, related genes and groups, interacting proteins, and other associated relationships for a list of supplied of gene names.

Drugs and Cancer

  • Genomics of Drug Sensitivity in Cancer is a research program to identify molecular and therapeutic biomarkers associated with cancers that can predict a response to anti-cancer drugs. Either genes or drug compounds may be searched.
  • LINCS Connectivity Map is an online database of gene expression changes in human cell lines that arise upon either genetic perturbation or drug treatment. The site is currently in beta testing and is not available as a public resource yet.