Network of Cancer Genes
The Network of Cancer Genes (NCG) is a freely accessible web resource of cancer genes and their associated properties.[1] The project started in 2010 and in August 2018 has reached its 6th release: NCG6.0. NCG6.0 reports information on 2,372 protein-coding cancer genes, including 711 known cancer genes from the Cancer Gene Census and the Vogelstein, Science 2013 list.[2] The remaining 1,661 cancer genes are candidate cancer genes annotated from the manual curation of 273 original publications. For each cancer gene NCG6.0 reports its system-level properties, the publications reporting it as a known or candidate cancer gene and information on the design of their cancer sequencing screens. In addition, the database provides annotations on 250 possible false positive genes, defined as candidate cancer genes whose association with cancer is likely to be spurious.[3][4]
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| Content | |
|---|---|
| Description | A web resource on systems-level properties of cancer genes |
| Organisms | Homo sapiens |
| Contact | |
| Research center | King's College London |
| Release date | August 2018 |
| Access | |
| Website | http://ncg.kcl.ac.uk |
| Miscellaneous | |
| Version | 6.0 |
Cancer sequencing screens
The 273 manually annotated publications in NCG6.0 describe a total 278 whole genome or whole exome cancer sequencing screens. These screenings included a total of 34,905 patients from 119 different cancer types. These include cancer sequencing screens of samples from 31 different anatomical sites, as well as 4 adult and 2 paediatric pan-cancer sequencing screens. NCG6.0 allows to perform advanced searches and retrieve information on cancer genes by: primary anatomical site, cancer type, and by sequencing screens or publication.
| Primary site | Cancer types |
|---|---|
| Blood | Diffuse large B-cell lymphoma, acute lymphocytic leukemia, chronic myeloid leukemia, multiple myeloma, chronic lymphocytic leukemia, cutaneous T cell lymphoma, T-cell leukemia/lymphoma, non-Hodgkin lymphoma, peripheral T-cell lymphoma, Burkitt's lymphoma, angioimmunoblastic T-cell lymphoma, acute myeloid leukemia, cutaneous DLBCL, acute monocytic leukemia, follicular lymphoma, chronic myelomonocytic leukemia, acute lymphoblastic leukemia, myeloproliferative neoplasm, acute promyelocytic leukemia, juvenile myelomonocytic leukemia, myelodysplasia, natural killer/T cell lymphoma, splenic marginal zone lymphoma, mediastinal B-cell lymphoma |
| Bladder | Bladder cancer |
| Breast | Breast cancer, triple negative breast cancer, breast fibroepithelial tumours, male breast cancer, breast fibroadenoma |
| Brain | Diffuse intrinsic pontine glioma, astrocytoma, paediatric high-grade glioma, glioblastoma, pan-glioma, meningioma, neuroblastoma, low grade glioma, paediatric low grade glioma, glioma, craniopharyngioma, intracranial germ cell, medulloblastoma, oligodendroglioma |
| Pancreas | Pancreatic cancer (all histologies), pancreatic ductal adenocarcinoma, pancreatic neuroendocrine tumours, pancreatic neoplastic cysts |
| Colon and Rectum | colorectal adenocarcinoma |
| Small Intestine | Ampullary adenocarcinoma, duodenal adenocarcinoma, neuroendocrine tumour |
| Hepatobiliary | Pan-liver, hepatocellular carcinoma, cholangiocarcinoma, biliary tract cancer, gallbladder carcinoma |
| Stomach | Gastric adenocarcinoma, diffuse gastric adenocarcinoma, mucinous gastric cancer |
| Lung | Small cell lung cancer, lung cancer (all histologies), lung adenocarcinoma, lung squamous cell carcinoma, non-small cell lung cancer |
| Head and Neck | Squamous head and neck cancer, nasopharyngeal carcinoma, ameloblastoma, oral squamous cell carcinoma, salivary gland adenocarcinoma |
| Prostate | Prostate cancer |
| Soft tissue | Angiosarcoma, soft tissue sarcoma, [rhabdomyosarcoma]] |
| Uterus | Endometrial cancer, uterine carcinosarcoma, serous endometrial cancer, leiomyoma, clear cell endometrial cancer |
| Peripheral Nervous System | Neuroblastoma, malignant peripheral nerve sheath tumour |
| Thymus | Thymic carcinoma |
| Skin | Melanoma, mucosal melanoma, desmoplastic melanoma, skin basal cell carcinoma |
| Kidney | Clear cell renal cancer, renal cancer (all histologies), non-clear cell renal cancer, papillary renal cell carcinoma, rhabdoid tumour, chromophobe renal cell carcinoma, renal angiomyolipoma |
| Adrenal gland | Adrenocortical adenoma, adrenocortical carcinoma, pheochromocytoma, paraganglioma |
| Esophagus | Esophageal squamous carcinoma, esophageal adenocarcinoma, esophageal (squamous and adenocarcinoma) |
| Bone | Osteosarcoma, Ewing sarcoma, chondrosarcoma, chondromyxoid fibroma, chondroblastoma, bone giant cell tumour |
| Parathyroid gland | Parathyroid carcinoma |
| Ovary | Ovarian cancer, ovarian serous carcinoma, ovarian clear-cell carcinoma, ovarian small-cell carcinoma |
| Penis | Penile squamous cancer |
| Thyroid | Papillary thyroid cancer, anaplastic thyroid carcinoma |
| Cervix | Cervical cancer (all histologies) |
| Testis | Testicular germ cell cancer |
| Retina | Retinoblastoma |
| Pleura | Malignant pleural mesothelioma |
| Uvea | Melanoma |
| Vascular system | Vascular cancer |
Systems level properties
Systems-level properties are properties of genes independent on an individual's gene function.[5] Some of these properties can be used to distinguish cancer genes from the rest of human genes.[1][6] The systems-level properties reported by NCG are:
- Duplicability: i.e. the presence of additional genomic sequences matching at least 60% of the gene sequence.[7]
- Evolutionary appearance: the presence or absence of ortholog genes in seven branches of the tree of life (Prokaryotes, Eukaryotes, Opisthokonts, Metazoans, Vertebrates, Mammals, Primates)
- Protein-protein interactions: a list of all human proteins interacting with the main protein encoded by the gene of interest and the number of complexes it is part of.
- microRNA-gene interactions: a list of experimentally verified interactions between the gene of interest and human miRNAs.
- Functional properties: a list of the functional classes of the gene of interest.
- Gene expression and protein expression: List of normal tissues and cancer cell lines the gene of interest is expressed in.
- Essentiality: a list of human cell lines in which the gene was found to be essential.
References
- Repana, Dimitra; Nulsen, Joel; Dressler, Lisa; Bortolomeazzi, Michele; Venkata, Santhilata Kuppili; Tourma, Aikaterini; Yakoleva, Anna; Palmieri, Tommaso; Ciccarelli, Francesca D. (2018-12-01). "The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens". bioRxiv: 389858. doi:10.1101/389858.
- Kinzler, Kenneth W.; Diaz, Luis A.; Zhou, Shibin; Velculescu, Victor E.; Papadopoulos, Nickolas; Vogelstein, Bert (2013-03-29). "Cancer Genome Landscapes". Science. 339 (6127): 1546–1558. Bibcode:2013Sci...339.1546V. doi:10.1126/science.1235122. ISSN 1095-9203. PMC 3749880. PMID 23539594.
- Lawrence, Michael S. (11 July 2013). "Mutational heterogeneity in cancer and the search for new cancer-associated genes". Nature. 499 (7457): 214–218. Bibcode:2013Natur.499..214L. doi:10.1038/nature12213. PMC 3919509. PMID 23770567.
- Bailey, Matthew H.; Tokheim, Collin; Porta-Pardo, Eduard; Sengupta, Sohini; Bertrand, Denis; Weerasinghe, Amila; Colaprico, Antonio; Wendl, Michael C.; Kim, Jaegil (2018). "Comprehensive Characterization of Cancer Driver Genes and Mutations". Cell. 174 (4): 1034–1035. doi:10.1016/j.cell.2018.07.034. ISSN 0092-8674. PMC 8045146. PMID 30096302.
- Ciccarelli, Francesca D. (2010-06-11). "The (r)evolution of cancer genetics". BMC Biology. 8 (1): 74. doi:10.1186/1741-7007-8-74. ISSN 1741-7007. PMC 2883958. PMID 20594288.
- D'Antonio, Matteo; Ciccarelli, Francesca D. (2013-05-29). "Integrated analysis of recurrent properties of cancer genes to identify novel drivers". Genome Biology. 14 (5): R52. doi:10.1186/gb-2013-14-5-r52. ISSN 1474-760X. PMC 4054099. PMID 23718799.
- Rambaldi, Davide; Giorgi, Federico M.; Capuani, Fabrizio; Ciliberto, Andrea; Ciccarelli, Francesca D. (2008). "Low duplicability and network fragility of cancer genes". Trends in Genetics. 24 (9): 427–430. doi:10.1016/j.tig.2008.06.003. ISSN 0168-9525. PMID 18675489.
- An, Omer; Dall'Olio, Giovanni M.; Mourikis, Thanos P.; Ciccarelli, Francesca D. (2016-01-04). "NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings". Nucleic Acids Research. 44 (D1): D992–D999. doi:10.1093/nar/gkv1123. ISSN 0305-1048. PMC 4702816. PMID 26516186.
- An, Omer; Pendino, Vera; D'Antonio, Matteo; Ratti, Emanuele; Gentilini, Marco; Ciccarelli, Francesca D. (2014-01-01). "NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes". Database. 2014: bau015. doi:10.1093/database/bau015. PMC 3948431. PMID 24608173.
- D'Antonio, Matteo; Pendino, Vera; Sinha, Shruti; Ciccarelli, Francesca D. (2012). "Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes". Nucleic Acids Res. 40 (Database issue): D978–83. doi:10.1093/nar/gkr952. PMC 3245144. PMID 22080562.
- Syed, Adnan S.; D'Antonio, Matteo; Ciccarelli, Francesca D. (2010). "Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes". Nucleic Acids Res. 38 (Database issue): D670–5. doi:10.1093/nar/gkp957. PMC 2808873. PMID 19906700.
External links
- NCG6.0: http://ncg.kcl.ac.uk
- NCG5.0: http://ncg.kcl.ac.uk/ncg5/
- NCG4.0: http://ncg.kcl.ac.uk/ncg4/
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