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Pancreatic Expression database: An existing tool for the mining of molecular alterations in pancreatic diseases
Posted by Claude_Chelala on 22 May 2009 at 10:02 GMT
Claude Chelala1*, Nicholas R Lemoine1, Stephan A Hahn2 and Tatjana Crnogorac-Jurcevic1
1 Centre for Molecular Oncology, Institute of Cancer & CR-UK Clinical Centre, Barts & The London School of Medicine (QMUL), Charterhouse Square London EC1M 6BQ, United Kingdom.
2 Molecular GI-Onkologie (MGO) & Department of Internal Medicine, University of Bochum, Germany.
* Corresponding author
We have read with great interest the article recently published in PLos Medicine describing a compendium of potential biomarkers of pancreatic cancer . The aim of such undertaking: ”is to develop a Web-based searchable database of all molecular alterations in pancreatic cancer—from the genome to the proteome—that will help initiate a systems medicine approach to cancer”, prompted us to highlight that we have ourselves already performed a similar task.
Indeed, our Institute has a long-standing interest in pancreatic adenocarcinoma and is a UK participating centre in the European Framework 6 project MolDiag-Paca , whose mission is to bring together leading groups in European pancreatic cancer research to develop novel molecular tools for the prevention and diagnosis of pancreatic cancer. We have constructed the Pancreatic Expression database [3,4,5] as a vital component of MolDiag-Paca working alongside the European leaders in pancreatic cancer field and discussing the research needs and questions that the database query interface should help answering. This was indeed a fantastic opportunity to develop a web interface from a pancreatic cancer scientist end-user perspective. Although our database in its current release does not include papers reporting a single gene/protein deregulation, it is a compilation of the largest expression profiling datasets of both pancreatic cancer and chronic pancreatitis, and also includes urine and plasma proteome data. The data content is constantly growing and a new release will include a new set of recent proteomic and genomic data.
Our paper  was ranked among the most highly accessed papers in BMC Genomics and we received more than one million visits to our database website  since it was first made public in July 2007. Relating to Harsha et al. , we have to note that our system could already be used for potential target discovery. For example, one could search and retrieve genes/proteins expressed only in pancreatic cancer and not in chronic pancreatitis and then ask which of these are present in urine and/or plasma. Such a query would be a first step for the discovery of non-invasive pancreatic cancer biomarkers from body fluids .
The Pancreatic Expression data management system is based on the BioMart technology [6,7], which is used in a number of high profile projects such as the International Cancer Genome Consortium (ICGC) , REACTOME pathways , HapMap genotypes  and PRIDE proteomics . BioMart software is also fully integrated into the main Ensembl website . Therefore, our system will store data alongside the Ensembl human genome annotations for genes and proteins, sequence, homologies, SNPs and the Human Protein Atlas antibody data . Moreover, the data stored in our platform can easily be integrated with the above data sources and any BioMart compliant data.
Our database provides access not only to bench researchers with a limited knowledge of bioinformatics, but also to bioinformatic and biostatistical experts. Firstly, access to the data is provided through a web-based query interface . Secondly, access is provided through the Bioconductor  package biomaRt , therefore allowing its easy interrogation within the open source R statistical environment  and its integration into any expression profiling experiment. The system could also be accessed programmatically through web services  and is referenced as a Linkout resource providing a Linkout annotation available at NCBI EntrezGene . Finally, the pancreatic resource is a DAS server providing DAS annotations for the wider community so it can be used in other resources or browsers such as Ensembl GeneView using GeneDAS protocol . These different levels of access together with our goal of full interoperability with major cancer research efforts will ensure wide national and international exposure to the Pancreatic Expression database.
Our database enables pancreatic researchers to mine and integrate the published data from multiple different sources into their current research programmes. Many examples of use including but not limited to pancreatic cancer biomarker discovery are already highlighted in our papers [3,4].
As any database is only as good as its content, we have invited the scientific community to contribute with both their suggestions for improvements and as well as providing their datasets. We would like to take this opportunity to also re-iterate our interest in collaborating with the international pancreatic cancer community around the world.
1. Harsha HC, Kandasamy K, Ranganathan P, Rani S, Ramabadran S, et al. (2009) A compendium of potential biomarkers of pancreatic cancer. PLoS Med 6: e1000046.
2. EU project MolDiag-Paca, http://www.moldiagpaca.eu.
3. Chelala C, Hahn SA, Whiteman HJ, Barry S, Hariharan D, 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 NR, Hahn SA, Crnogorac-Jurcevic T (2009) A Web-Based Platform for Mining Pancreatic Expression Datasets. Pancreatology 9: 340-343.
5. Pancreatic Expression database, www.pancreasexpression.or....
6. Haider S, Ballester B, Smedley D, Zhang J, Rice P, et al. (2009) BioMart Central Portal--unified access to biological data. Nucleic Acids Res.
7. Smedley D, Haider S, Ballester B, Holland R, London D, et al. (2009) BioMart--biological queries made easy. BMC Genomics 10: 22.
8. International Cancer Genome Consortium (ICGC), http://www.icgc.org.
9. REACTOME pathways, http://reactome.org/cgi-b....
10. HapMap genotypes, http://hapmart.hapmap.org....
11. PRIDE proteomics, http://www.ebi.ac.uk/prid....
12. Ensembl, www.ensembl.org.
13. Human Protein Atlas, www.proteinatlas.org.
14. Pancreatic Expression database web-based query interface, www.pancreasexpression.or....
15. Bioconductor, www.bioconductor.org.
16. Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, et al. (2005) BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21: 3439-3440.
17. R project, www.r-project.org.
18. Pancreatic Expression database access through web services, www.pancreasexpression.or....
19. NCBI EntrezGene, www.ncbi.nlm.nih.gov/site....