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

Rosalind J Cutts; Emanuela Gadaleta; Nicholas R Lemoine; Claude Chelala

doi:10.1093/database/bar024

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

Database (Oxford). 2011 Jun 11:2011:bar024. doi: 10.1093/database/bar024. Print 2011.

Authors

Rosalind J Cutts¹, Emanuela Gadaleta, Nicholas R Lemoine, Claude Chelala

Affiliation

¹ Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods*
DNA Copy Number Variations / genetics
Database Management Systems*
Databases, Genetic*
Gene Expression Regulation, Neoplastic
Humans
Internet
MicroRNAs / genetics
Pancreatic Neoplasms / genetics*
Search Engine*
Software*

Substances

MicroRNAs

Abstract

Publication types

MeSH terms

Substances

Grants and funding