Using BioMart as a framework to manage and query pancreatic cancer data

Database

Volumn 2011, Issue , 2011, Pages

  Cutts, Rosalind J ^a   Gadaleta, Emanuela ^a   Lemoine, Nicholas R ^a   Chelala, Claude ^a  

^a QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; COPY NUMBER VARIATION; DATA BASE; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; HUMAN; INTERNET; METHODOLOGY; PANCREAS TUMOR; SEARCH ENGINE;

COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; DNA COPY NUMBER VARIATIONS; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; INTERNET; MICRORNAS; PANCREATIC NEOPLASMS; SEARCH ENGINE; SOFTWARE;

EID: 80053929641     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bar024     Document Type: Article

References (20)

1. Gadaleta, E., Lemoine, N. R. and Chelala, C. (2011) Online resources of cancer data: barriers, benefits and lessons. Brief Bioinform., 12, 52-63.
2. Haider, S., Ballester, B., Smedley, D. et al. (2009) BioMart Central Portal-unified access to biological data. Nucleic Acids Res., 37, W23-W27.
3. Chelala, C., Hahn, S. A., Whiteman, H. J. et al. (2007) Pancreatic Expression database: A generic model for the organization, integration and mining of complex cancer datasets. BMC Genomics, 8, 439.
4. Chelala, C., Lemoine, N. R., Hahn, S. A. et al. (2009) A web-based platform for mining pancreatic expression datasets. Pancreatology, 9, 340-343.
5. Cutts, R. J., Gadaleta, E., Hahn, S. A. et al. (2011) The Pancreatic Expression database: 2011 update. Nucleic Acids Res., 39, D1023-D1028.
6. Dowell, R. D., Jokerst, R. M., Day, A., Eddy, S. R. and Stein, L. (2001) The distributed annotation system. BMC Bioinformatics, 2, 7.
7. Hubbard, T. J., Aken, B. L., Ayling, S. et al. (2009) Ensembl 2009.
8. Nucleic Acids Res., 37, D690-D697.
9. Tatusova, T. (2010) Genomic databases and resources at the National Center for Biotechnology Information. Methods Mol. Biol., 609, 17-44.
10. BioConductor. www.bioconductor.org (14 April 2011, date last accessed).
11. Giardine, B., Riemer, C., Hardison, R. C. et al. (2005) Galaxy: A platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455. (Pubitemid 41400913)
12. Cline, M. S., Smoot, M., Cerami, E. et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc., 2, 2366-2382.
13. Hudson, T. J., Anderson, W. and Artez, A. (2011) International network of cancer genome projects. Nature, 464, 993-998.
14. ICGC Data Portal. http://dcc.icgc.org (20 April 2011, date last accessed).
15. Hruban, R. H., Maitra, A. and Goggins, M. (2008) Update on pancreatic intraepithelial neoplasia. Int. J. Clin. Exp. Pathol., 1, 306-316.
16. Hruban, R. H., Adsay, N. V., Albores-Saavedra, J. et al. (2001) Pancreatic intraepithelial neoplasia: A new nomenclature and classification system for pancreatic duct lesions. Am. J. Surg. Pathol., 25, 579-586. (Pubitemid 32423354)
17. Nakata, K., Nagai, E., Ohuchida, K. et al. (2010) S100P is a novel marker to identify intraductal papillary mucinous neoplasms. Hum. Pathol., 41, 824-831.
18. Crnogorac-Jurcevic, T., Missiaglia, E., Blaveri, E. et al. (2003) Molecular alterations in pancreatic carcinoma: expression profiling shows that dysregulated expression of S100 genes is highly prevalent. J. Pathol., 201, 63-74. (Pubitemid 37121204)
19. Matthews, L., Gopinath, G., Gillespie, M. et al. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res., 37, D619-D622.
20. Forbes, S. A., Bindal, N., Bamford, S. et al. (2011) COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Res., 39, D945-D950.