Contents [hide] 

  • Overview
  • Statistics
    1. Number of cancer genes by cancer types
    2. Number of mutations by cancer types
    3. Number of CNVs by cancer types
    4. Number of drug-gene interactions by cancer types
  • Datasets

    Datasets used in CCG, including published papers and public databases.

  • Usages
    1. Search cancer genes
    2. Browse the database
    3. Visualize results
  • Future extensions
    1. Add data
    2. Exploit the cancer genes
    3. Add online tools

Overview

The Catalogue of Cancer Genes (CCG) database is a comprehensive inventory of cancer genes. It includes both well-supported and putative cancer protein-coding genes and lncRNAs collected from literature research of published papers and public databases. In addition, uniform genomic aberration information, such as somatic mutations copy number variations information, and drug-gene interactions were assigned to cancer genes in the database. CCG represents an effort on integrative assembling of well-supported and putative coding and noncoding cancer genes and takes advantages of high-through put sequencing results on large population. CCG will help cancer researches and facilitate the understanding of cancer mechanisms.

Statistics

Datasets

Data provided in CCG were collected from 84 published papers and database. The data sets were listed as following:

Resource type Reference/Resource Category
Cancer coding genes Cancer Gene Census Published database
Putative cancer coding genesZang ZJ. et.al., Nat Genet., 2012Published paper
Putative cancer coding genesChan-On W. et.al., Nat Genet., 2013Published paper
Putative cancer coding genesTCGA, N Engl J Emd.,2013Published paper
Putative cancer coding genesLeiserson MD. et.al., Nat Genet., 2015Published paper
Putative cancer coding genesWang L. et.al., N Engl J Med., 2011Published paper
Putative cancer coding genesRobinson D. et.al., Cell, 2015Published paper
Putative cancer coding genesTCGA, Nature, 2013Published paper
Putative cancer coding genesSato Y. et.al., Nat Genet., 2013Published paper
Putative cancer coding genesLohr JG. et.al., Cancer Cell, 2014Published paper
Putative cancer coding genesSanchez-Garcia F. et.al., Cell, 2014Published paper
Putative cancer coding genesTCGA, Nature, 2014Published paper
Putative cancer coding genesRubio-Perez C. et.al., Cancer Cell, 2015Published paper
Putative cancer coding genesMcGranahan N. et.al., Sci Transl Med., 2015Published paper
Putative cancer coding genesYoshida K. et.al., Nature, 2011Published paper
Putative cancer coding genesTCGA, Nature,2012Published paper
Putative cancer coding genesKandoth C. et.al., Nature, 2013Published paper
Putative cancer coding genesLohr JG. et.al., PNAS, 2012Published paper
Putative cancer coding genesEllis MJ. et.al., Nature, 2012Published paper
Putative cancer coding genesAhn SM. et.al., hepatology, 2014Published paper
Putative cancer coding genesLawrence MS. et.al., Nature, 2014Published paper
Putative cancer coding genesParsons DW. et.al., Science, 2008Published paper
Putative cancer coding genesRobinson G. et.al., Nature, 2012Published paper
Putative cancer coding genesAgrawal N. et.al., Science, 2011Published paper
Putative cancer coding genesTCGA, Nature, 2014Published paper
Putative cancer coding genesPasqualucci L. et.al., Nat Genet. 2011Published paper
Putative cancer coding genesStransky N. et.al., Science, 2011Published paper
Putative cancer coding genesBiankin AV. et.al., Nature, 2012Published paper
Putative cancer coding genesGuo G. et.al., Nat Genet., 2013Published paper
Putative cancer coding genesTCGA, Nature, 2014Published paper
Putative cancer coding genesWang K. et.al. Nat Genet., 2014Published paper
Putative cancer coding genesKovac M. et.al., Nat Commun., 2015Published paper
Putative cancer coding genesBanerji S. et.al., Nature, 2012Published paper
Putative cancer coding genesBarretina J. et.al., Nat Genet., 2010Published paper
Putative cancer coding genesHo AS. et.al., Nat Genet., 2013Published paper
Putative cancer coding genesHuang J. et.al., Nat Genet., 2012Published paper
Putative cancer coding genesTCGA, Nature, 2012Published paper
Putative cancer coding genesRudin CM. et.al., Nat Genet., 2012Published paper
Putative cancer coding genesPeifer M. et.al., Nat Genet., 2012Published paper
Putative cancer coding genesBerger MF. et.al., Nature, 2012Published paper
Putative cancer coding genesPuente XS. et.al., Nature, 2011Published paper
Putative cancer coding genesGuo G. et.al., Nat Genet., 2011Published paper
Putative cancer coding genesBarbieri CE. et.al., Nat Genet., 2012Published paper
Putative cancer coding genesTCGA, Nature, 2011Published paper
Putative cancer coding genesSchulze K. et.al., Nat Genet., 2015Published paper
Putative cancer coding genesHodis E. et.al., Cell, 2012Published paper
Putative cancer coding genesQuesada V. et.al., Nat Genet., 2011Published paper
Putative cancer coding genesLin DC. et.al., Nat Genet., 2014Published paper
Putative cancer coding genesSong Y. et.al., Nature, 2014Published paper
Putative cancer coding genesDing L. et.al., Nature, 2008Published paper
Putative cancer coding genesSuzuki H. et.al., Nat Genet., 2015Published paper
Putative cancer coding genesSeshagiri S. et.al., Nature, 2012Published paper
Putative cancer coding genesKim PH. et.al., Eur Urol., 2015Published paper
Putative cancer coding genesChapman MA. et.al., Nature, 2011Published paper
Putative cancer coding genesSchwartzentruber J. et.al., Nature, 2012Published paper
Putative cancer coding genesTamborero D. et.al., Sci Rep, 2013Published paper
Putative cancer coding genesTCGA, Cell, 2014Published paper
Putative cancer coding genesCheng WC. et.al., Nucleic Acids Res., 2014Published paper
Putative cancer coding genesImielinski M. et.al., Cell, 2012Published paper
Putative cancer coding genesJones DT. et.al., Nature, 2012Published paper
Putative cancer coding genesFabbri G. et.al., J Exp Med., 2011Published paper
Putative cancer coding genesJelinic P. et.al., Nat Genet., 2014Published paper
Putative cancer coding genesGrasso CS. et.al., Nature, 2012Published paper
Putative cancer coding genesShah SP. et.al., Nature, 2012Published paper
Putative cancer coding genesLi M. et.al., Nat Genet., 2011Published paper
Putative cancer coding genesZhang J. et.al., Nature, 2012Published paper
Putative cancer coding genesOng CK. et.al., Nat Genet., 2012Published paper
Putative cancer coding genesTaylor BS. et.al., Cancer Cell, 2010Published paper
Putative cancer coding genesKrauthammer M. et.al, Nat Genet., 2012Published paper
Putative cancer coding genesFujimoto A. et.al., Nat Genet, 2012Published paper
Putative cancer coding genesTCGA, Nature, 2012Published paper
Putative cancer coding genesStephens PJ. et.al., Nature, 2012Published paper
Putative cancer coding genesTCGA, Nautre, 2013Published paper
Putative cancer coding genesCambus JP. et.al., Rev Med Interne., 2013Published paper
Putative cancer coding genesWang K. et.al., Nat Genet., 2011Published paper
Putative cancer coding genesTCGA, Nature, 2008Published paper
Putative cancer coding genesBrennan CW. et.al., Cell, 2013Published paper
Putative cancer coding genesPugh TJ. et.al., Nature, 2012Published paper
Putative cancer coding genesGuichard C. et.al., Nat Genet., 2012Published paper
Cancer lncRNAs Sahu A. et.al., Trends in Cancer, 2015 Published paper
Putative cancer lncRNAs lnc2cancer database Published database

Usage

  1. Search cancer genes

    Our database is user-frienly designed. Users can get the gene general information as well as genomic aberration information simply by inputting the gene symbol/gene ID into query inbox and clicking the search button. We use a autocomplete library to help users to select the gene name.

  2. Browse the database

    Users can also have a glance of the whole cancer genes list in the “Browse” page where the complete list of cancer genes were shown. The cancer genes are classified into two groups: gene lists by protein-coding abilities and by primary sites.

  3. Visualize results

Future extensions

  1. Add data

    As previous study shown, the inventory of cancer genes for now is far from complete. The number of cancer genes increases steadily with sample size, more genome wide screening in larger sample size and larger numbers of cancer types will identify more cancer genes. In addition, thousands of lncRNAs are indicated to play important roles in cancers, but only limited numbers of them have been identified. More cancer genes are waiting to be characterized. As the implementation of the precise genome projects and other population based huge genomic studies continue, more genomic data will be generated in the near future. We anticipate that plenty of cancer genes will be identified in the future as a result of the booming of whole-genome wide studies in large population.

    We will continue to curate novel validated cancer protein-coding genes as well as cancer lncRNAs from all cancer types and update the database. Functional annotations, such as gene ontology analysis and pathway analysis, will help users to better interpret cancer genes. Molecular interactions, such as gene products with miRNA and RNA binding proteins, will be updated in the future versions as well.

  2. Exploit the cancer genes
  3. Machine learning and deep learning is an astonishing powerful strategy to make discovery on big data. The application of machine learning and deep learning on biology has successfully solved many problems. For instance, Margaret A. Shipp et.al (Nat Med. 2002) and Shuangtao Zhao et.al. (Cancer Med. 2016) classified diffuse large B-cell lymphoma patients by gene expression profiles and predicted the outcome with machine learning methods. In the future, we will adapt the machine learning on cancer genes identificaiton and outcome prediction with a panel of cancer biomarker genes.

  4. Add online tools
  5. The secondary RNA structures are believed affecting functions of genes, especially lncRNAs. Mutations and SNPs on genes would change the secondary structure of genes. Previously, we have developed a algorithm that use experimental data to enhance the secondary structure predictions (Yang Wu et.al. Nucleic Acids Research, 2015). In the future, we would integrate the online prediction tools for cancer genes.

Copyright © 2016 Lu Lab, School of Life Sciences, Tsinghua University, China