Article thumbnail

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

By Rosalind J. Cutts, Emanuela Gadaleta, Nicholas R. Lemoine and Claude Chelala

Abstract

We describe the Pancreatic Expression Database (PED), the first cancer database originally designed based on the BioMart infrastructure. The PED portal brings together multidimensional pancreatic cancer data from the literature including genomic, proteomic, miRNA and gene expression profiles. Based on the BioMart 0.7 framework, the database is easily integrated with other BioMart-compliant resources, such as Ensembl and Reactome, to give access to a wide range of annotations alongside detailed experimental conditions. This article is intended to give an overview of PED, describe its data content and work through examples of how to successfully mine and integrate pancreatic cancer data sets and other BioMart resources

Topics: Original Article
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:3114646
Provided by: PubMed Central

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles

Citations

  1. (2009). A web-based platform for mining pancreatic expression datasets.
  2. (2009). BioMart Central Portal–unified access to biological data.
  3. (2011). COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer.
  4. (2009). Ensembl
  5. (2005). Galaxy: a platform for interactive large-scale genome analysis.
  6. (2010). Genomic databases and resources at the National Center for Biotechnology Information. Methods Mol.
  7. (2007). Integration of biological networks and gene expression data using Cytoscape.
  8. (2011). International network of cancer genome projects.
  9. (2003). Molecular alterations in pancreatic carcinoma: expression profiling shows that dysregulated expression of S100 genes is highly prevalent.
  10. (2011). Online resources of cancer data: barriers, benefits and lessons.
  11. (2007). Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets.
  12. (2001). Pancreatic intraepithelial neoplasia: a new nomenclature and classification system for pancreatic duct lesions.
  13. (2009). Reactome knowledgebase of human biological pathways and processes.
  14. (2010). S100P is a novel marker to identify intraductal papillary mucinous neoplasms.
  15. (2001). The distributed annotation system.
  16. (2011). The Pancreatic Expression database:
  17. (2008). Update on pancreatic intraepithelial neoplasia.