The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens

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Abstract

The Network of Cancer Genes (NCG) is a manually curated repository of 2372 genes whose somatic modifications have known or predicted cancer driver roles. These genes were collected from 275 publications, including two sources of known cancer genes and 273 cancer sequencing screens of more than 100 cancer types from 34,905 cancer donors and multiple primary sites. This represents a more than 1.5-fold content increase compared to the previous version. NCG also annotates properties of cancer genes, such as duplicability, evolutionary origin, RNA and protein expression, miRNA and protein interactions, and protein function and essentiality. NCG is accessible at http://ncg.kcl.ac.uk/.

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The online version of this article (10.1186/s13059-018-1612-0) contains supplementary material, which is available to authorized users.

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miRecords: an integrated resource for microRNA–target interactions

Feifei Xiao, Zhixiang Zuo, Guoshuai Cai … (2009)

MicroRNAs (miRNAs) are an important class of small noncoding RNAs capable of regulating other genes’ expression. Much progress has been made in computational target prediction of miRNAs in recent years. More than 10 miRNA target prediction programs have been established, yet, the prediction of animal miRNA targets remains a challenging task. We have developed miRecords, an integrated resource for animal miRNA–target interactions. The Validated Targets component of this resource hosts a large, high-quality manually curated database of experimentally validated miRNA–target interactions with systematic documentation of experimental support for each interaction. The current release of this database includes 1135 records of validated miRNA–target interactions between 301 miRNAs and 902 target genes in seven animal species. The Predicted Targets component of miRecords stores predicted miRNA targets produced by 11 established miRNA target prediction programs. miRecords is expected to serve as a useful resource not only for experimental miRNA researchers, but also for informatics scientists developing the next-generation miRNA target prediction programs. The miRecords is available at http://miRecords.umn.edu/miRecords.

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The BioGRID interaction database: 2017 update

Andrew Chatr-aryamontri, Rose Oughtred, Lorrie Boucher … (2016)

The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2016 (build 3.4.140), the BioGRID contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. BioGRID curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases. To facilitate network-based approaches to drug discovery, BioGRID now incorporates 27 501 chemical–protein interactions for human drug targets, as drawn from the DrugBank database. A new dynamic interaction network viewer allows the easy navigation and filtering of all genetic and protein interaction data, as well as for bioactive compounds and their established targets. BioGRID data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases.

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CORUM: the comprehensive resource of mammalian protein complexes—2009

Andreas Ruepp, Brigitte Waegele, Martin Lechner … (2010)

CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The new CORUM 2.0 release encompasses 2837 protein complexes offering the largest and most comprehensive publicly available dataset of mammalian protein complexes. The CORUM dataset is built from 3198 different genes, representing ∼16% of the protein coding genes in humans. Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex. Recent developments include mapping of functional annotation to Gene Ontology terms as well as cross-references to Entrez Gene identifiers. In addition, a ‘Phylogenetic Conservation’ analysis tool was implemented that analyses the potential occurrence of orthologous protein complex subunits in mammals and other selected groups of organisms. This allows one to predict the occurrence of protein complexes in different phylogenetic groups. CORUM is freely accessible at (http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html).

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Contributors

Dimitra Repana: dimitra.repana@crick.ac.uk

Joel Nulsen: joel.nulsen@crick.ac.uk

Lisa Dressler: lisa.dressler@crick.ac.uk

Michele Bortolomeazzi: michele.bortolomeazzi@crick.ac.uk

Santhilata Kuppili Venkata: santhilata.kuppili_venkata@crick.ac.uk

Aikaterini Tourna: aikaterini.tourna@crick.ac.uk

Anna Yakovleva: yakovleva.anna@gmail.com

Tommaso Palmieri: tommaso.palmieri@crick.ac.uk

Francesca D. Ciccarelli:

ORCID: http://orcid.org/0000-0002-9325-0900

+44 (0)20 7848 6616 , francesca.ciccarelli@crick.ac.uk , francesca.ciccarelli@kcl.ac.uk

Journal

Journal ID (nlm-ta): Genome Biol

Journal ID (iso-abbrev): Genome Biol

Title: Genome Biology

Publisher: BioMed Central (London )

ISSN (Print): 1474-7596

ISSN (Electronic): 1474-760X

Publication date (Electronic): 3 January 2019

Publication date PMC-release: 3 January 2019

Publication date Collection: 2019

Volume: 20

Electronic Location Identifier: 1

Affiliations

[1 ]ISNI 0000 0004 1795 1830, GRID grid.451388.3, Cancer Systems Biology Laboratory, , The Francis Crick Institute, ; London, NW1 1AT UK

[2 ]ISNI 0000 0001 2322 6764, GRID grid.13097.3c, School of Cancer and Pharmaceutical Sciences, , King’s College London, ; London, SE1 1UL UK

Author information

Francesca D. Ciccarelli http://orcid.org/0000-0002-9325-0900

Article

Publisher ID: 1612

DOI: 10.1186/s13059-018-1612-0

PMC ID: 6317252

PubMed ID: 30606230

SO-VID: b9fdcdaf-1142-4183-a11f-721e0911f073

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 11 August 2018

Date accepted : 12 December 2018

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100000289, Cancer Research UK;

Award ID: C43634/A25487

Award Recipient : Francesca D. Ciccarelli

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ScienceOpen disciplines: Genetics

Keywords: cancer genomics screens,cancer genes,cancer heterogeneity,systems-level properties

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ScienceOpen disciplines: Genetics

Keywords: cancer genomics screens, cancer genes, cancer heterogeneity, systems-level properties

The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens

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G3: Genes|Genomes|Genetics

Most cited references 40

miRecords: an integrated resource for microRNA–target interactions

The BioGRID interaction database: 2017 update

CORUM: the comprehensive resource of mammalian protein complexes—2009

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