The International Cancer Research Portfolio (ICRP) is a database of research funded by cancer research organizations throughout the world. The ICRP public web site allows the public at-large to view and browse information about research supported by cancer funding organizations in the United States (US), the United Kingdom (UK) and Canada
The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer providing online access to a variety of information on tumor models, genetic factors, tumor pathology, etc.
The Connectivity Map uses computer algorithms and genome-wide expression data to explore the connection between diseases, genes, and drugs. Cmap is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes. The aim of theConnectivity
The Provocative Questions initiative from NCI asks investigators to propose important but non-obvious questions in cancer research that need attention but would usually find it difficult to get.NCI has issued a request for applications and provisionally set aside US$15 million from the budget for fiscal year 2012 to support the best ideas for answering any of the questions chosen from a list of 24.
The cBio Cancer Genomics Portal provides visualization and analysis for working with data from TCGA and other data sets and provides download of large-scale cancer genomics data sets. You can query this user-friendly portals maintained by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center by entering the name of one or more genes. The output is a list of cancer studies of different tumor types; click on a study, and then on View Cancer Study Details, to call up a graphicâ
DoCM is database of curated mutations in cancer, an open-source, openly licensed resource to enable the cancer research community to aggregate, store, and track biologically important cancer variants with provenance supported by the literature (see Ainscough BY et al., Nat Meth 13:806, 2016)
The International Cancer Genome Consortium (ICGC) Data Portal allows researchers to access mutation and expression data for specific genes, or to scroll through data sets collected so far on 24 types of cancers by project teams in 9 countries. It represents a good starting point to check for known mutations and other aberrations in a gene of interest.
SurvExpress is a comprehensive gene expression database and web-based tool providing survival analysis and risk assessment in cancer datasets using a biomarker gene list as input. outcomes. SurvExpress provides survival analysis and risk assessment in cancer datasets using a biomarker gene list as input. The analysis requires only the list of genes and can be performed in approximately one minute per dataset (Aguirre-Gamboa et al, Plos one 8:e74250, 2013).
The UC Santa Cruz Cancer Genomics Browser is a suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It displays side-by-side heat maps of genomic data such as gene expression and copy number changes, and clinical data for a long list of cancer data sets, along with a feature that enables researchers to look for genomic variations that correlate with clinical outcomes.
The Cancer Genome Atlas (TCGA) Data Portal provides a platform to retrieve information on somatic mutations, or other data types such as copy number, DNA methylation, and gene expression, for a number of tumor types. It contains clinical information, genomic characterization data, and high-throughput sequencing analysis of the tumor genomes.TCGA updates as soon as new data become available.
CaSNP is a comprehensive collection of copy number alteration (CNA) from SNP arrays.With a user input of region or gene of interest, CaSNP will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study, and provide links to download the data or visualize it in UCSC Genome Browser
The server from MSKCC predicts the functional impact (high, medium, low, or neutral) of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. MutationAssessor looks at
conservation across all the homologs of a protein and also it takes into account the
conservation within just the closest homologs, which is called â€œspecifici
Regulome Explorer is a set of tools that facilitates the integrative exploration of associations in clinical and molecular TCGA data by providing a wide-ranging view of connections between mutations, expression level changes, and clinical outcomes. The tools were developed by by the Institute for Systems Biology in Seattle, Washington, and MD Anderson Cancer Center at the University of Texas in Houston.