Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis

Database

Volumn 2015, Issue , 2015, Pages

  Wu, Tsung Jung ^a   Schriml, Lynn M ^b   Chen, Qing Rong ^c   Colbert, Maureen ^d   Crichton, Daniel J ^d   Finney, Richard ^c   Hu, Ying ^c   Kibbe, Warren A ^c   Kincaid, Heather ^d   Meerzaman, Daoud ^c   Mitraka, Elvira ^b   Pan, Yang ^a   Smith, Krista M ^a   Srivastava, Sudhir ^c   Ward, Sari ^e   Yan, Cheng ^a   Mazumder, Raja ^a  

^a GEORGE WASHINGTON UNIVERSITY SCHOOL OF MEDICINE AND HEALTH SCIENCES   (United States)

^b UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

^d CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^e WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BIOLOGICAL ONTOLOGY; DATA MINING; FACTUAL DATABASE; HUMAN; NEOPLASM;

ANIMALS; BIOLOGICAL ONTOLOGIES; DATA MINING; DATABASES, FACTUAL; HUMANS; NEOPLASMS;

EID: 84943179865     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bav032     Document Type: Article

References (47)

1. WHO. (2014) World Health Organization: Cancer. Vol. 2014. http://www.who.int/mediacentre/factsheets/fs297/en/ (17 October 2014, date last accessed).
2. Liotta, L.A. (1992) Cancer cell invasion and metastasis. Sci Am. 1992 Feb;266(2):54-59, 62-63.
3. NCI. (2014) What Is Cancer. http://www.cancer.gov/cancertopics/cancerlibrary/what-is-cancer.
4. Evan, G.I. and Vousden, KH. (2001) Proliferation, cell cycle and apoptosis in cancer. Nature, 411, 342-348.
5. Elmore, S. (2007) Apoptosis: a review of programmed cell death. Toxicol. Pathol., 35, 495-516.
6. Majno, G. and Joris, I. (1995) Apoptosis, oncosis, and necrosis. An overview of cell death. Am. J. Pathol., 146, 3-15.
7. Peter, M.E. (2011) Programmed cell death: apoptosis meets necrosis. Nature, 471, 310-312.
8. Friedberg, E.C., Walker, G.C. and Siede, W. (1995) DNA repair and mutagenesis. ASM Press, Washington, D.C.
9. Klaunig, J.E., Kamendulis, L.M. and Hocevar, B.A. (2010) Oxidative stress and oxidative damage in carcinogenesis. Toxicol Pathol, 38, 96-109.
10. Sudhakar, A. (2009) History of cancer, ancient and modern treatment methods. J. Cancer Sci. Ther., 1, 1-4.
11. Golub, T.R., Slonim, D.K., Tamayo, P. et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286, 531-537.
12. Galon, J., Pages, F., Marincola, F.M. et al. (2012) Cancer classification using the immunoscore: a worldwide task force. J. Transl. Med., 10, 205.
13. Libenson, L. and Jena, M. (1978) On the definition, cause and nomenclature of cancer. Med Hypotheses, 4, 277-281.
14. Edge, S.B. and Compton, C.C. (2010) The American Joint Committee on Cancer: the 7th edition of the AJCC cancer staging manual and the future of TNM. Ann. Surg. Oncol., 17, 1471-1474.
15. Sobin, L.H. and Fleming, I.D. (1997) TNM classification of malignant tumors, fifth edition (1997). Union Internationale Contre le Cancer and the American Joint Committee on Cancer. Cancer, 80, 1803-1804.
16. NCI. (2013) Cancer Staging. Vol. 2014, http://www.cancer.gov/cancertopics/factsheet/detection/staging (17 October 2014, date last accessed).
17. Pan, Y., Karagiannis, K., Zhang, H. et al. (2015) Human germline and pan-cancer variomes and their distinct functional profiles. Nucleic Acids Res., 42, 11570-11588.
18. Weinstein, J.N., Collisson, E.A., Mills, G.B. et al. (2013) The cancer genome atlas pan-cancer analysis project. Nat. Genet., 45, 1113-1120.
19. Hoadley, K.A., Yau, C., Wolf, D.M. et al. (2014) Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell, 158, 929-944.
20. Sveen, A., Johannessen, B., Teixeira, M.R. et al. (2014) Transcriptome instability as a molecular pan-cancer characteristic of carcinomas. BMC Genomics, 15, 672.
21. Han, L., Yuan, Y., Zheng, S. et al. (2014) The Pan-cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes. Nat. Commun., 5, 3963.
22. Akbani, R., Ng, P.K., Werner, H.M. et al. (2014) A pan-cancer proteomic perspective on the cancer genome atlas. Nat. commun., 5, 3887.
23. Jia, P., Pao, W. and Zhao, Z. (2014) Patterns and processes of somatic mutations in nine major cancers. BMC Med. Genomics, 7, 11.
24. Kandoth, C., McLellan, M.D., Vandin, F. et al. (2013) Mutational landscape and significance across 12 major cancer types. Nature, 502, 333-339.
25. Wu, T.J., Shamsaddini, A., Pan, Y. et al. (2014) A framework for organizing cancer-related variations from existing databases, publications and NGS data using a high-performance integrated virtual environment (HIVE). Database, 2014, bau022.
26. Bard, J.B. and Rhee, S.Y. (2004) Ontologies in biology: design, applications and future challenges. Nat. Rev. Genet., 5, 213-222.
27. WHO. (1992) ICD-10 Classifications of Mental and Behavioural Disorder: Clinical Descriptions and Diagnostic Guidelines. World Health Organisation, Geneva, Vol. 16, pp. 14-16.
28. Cote, R.A. and Robboy, S. (1980) Progress in medical information management. Systematized nomenclature of medicine (SNOMED). JAMA, 243, 756-762.
29. Rogers, F.B. (1963) Medical subject headings. Bull. Med. Libr. Assoc., 51, 114-116.
30. Bodenreider, O. (2004) The unified medical language system (UMLS): integrating biomedical terminology. Nucleic Acids Res., 32, D267-D270.
31. Harris, S.T., Zeng, X. and Ford, L. (2011) International classification of diseases, 10th revision: it's coming, ready or not. Health Care Manag., 30, 227-235.
32. Rubin, D.L., Shah, N.H. and Noy, N.F. (2008) Biomedical ontologies: a functional perspective. Brief. Bioinform., 9, 75-90.
33. Ashburner, M., Ball, C.A., Blake, J.A. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
34. Davis, M.J., Sehgal, M.S., Ragan, M.A. (2010) Automatic, context-specific generation of gene ontology slims. BMC Bioinformatics, 11, 498.
35. Forbes, S.A., Bhamra, G., Bamford, S. et al. (2008) The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet, Chapter 10, Unit 10, 11.
36. Chin, L., Hahn, W.C., Getz, G. et al. (2011) Making sense of cancer genomic data. Genes Dev., 25, 534-555.
37. Hudson, T.J., Anderson, W., Artez, A. et al. (2010) International network of cancer genome projects. Nature, 464, 993-998.
38. Gonzalez-Perez, A., Perez-Llamas, C., Deu-Pons, J. et al. (2013) IntOGen-mutations identifies cancer drivers across tumor types. Nat. Methods, 10, 1081-1082.
39. (1999) Early detection research network in the US. Dis. Markers, 15, 213-219.
40. Wan, Q., Dingerdissen, H., Fan, Y. et al. (2015) BioXpress: an integrated RNA-seq derived gene expression database for pancancer analysis. Database.
41. Kibbe, W.A., Arze, C., Felix, V. et al. (2014) Disease ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res. 43, D1071-D1078.
42. Forbes, S.A., Beare, D., Gunasekaran, P. et al. (2014) COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43, D805-D811.
43. Zhang, J., Baran, J., Cros, A. et al. (2011) International Cancer Genome Consortium Data Portal-a one-stop shop for cancer genomics data. Database, 2011.
44. NCI. (2014) TARGET: Therapeutically Applicable Research to Generate Effective Treatments. https://ocg.cancer.gov/s/target. (23 September 2014, date last accessed).
45. NCI. (2014) EDRN: Early Detection Research Network. http://edrn.nci.nih.gov/. (10 August 2014, date last accessed).
46. Krzywinski, M., Schein, J., Birol, I. et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res., 19, 1639-1645.
47. Vogelstein, B., Papadopoulos, N., Velculescu, V.E. et al. (2013) Cancer genome landscapes. Science, 339, 1546-1558.