The pancreatic expression database: recent extensions and updates

Abstract

The Pancreatic Expression Database (PED, http://www.pancreasexpression.org) is the only device currently available for mining of pancreatic cancer literature data. It brings together the largest collection of multidimensional pancreatic data from the literature including genomic, proteomic, microRNA, methylomic and transcriptomic profiles. PED allows the user to ask specific questions on the observed levels of deregulation among a broad range of specimen/experimental types including healthy/patient tissue and body fluid specimens, cell lines and murine models as well as related treatments/drugs data. Here we provide an update to PED, which has been previously featured in the Database issue of this journal. Briefly, PED data content has been substantially increased and expanded to cover methylomics studies. We introduced an extensive controlled vocabulary that records specific details on the samples and added data from large-scale meta-analysis studies. The web interface has been improved/redesigned with a quick search option to rapidly extract information about a gene/protein of interest and an upload option allowing users to add their own data to PED. We added a user guide and implemented integrated graphical tools to overlay and visualize retrieved information. Interoperability with biomart-compatible data sets was significantly improved to allow integrative queries with pancreatic cancer data.

Figure 1.

Data growth in PED. Data for the three releases are shown.

Figure 2.

Integrated graphical view of transcriptomic and genomic changes observed between pancreatic ductal adenocarcinoma and normal tissue samples. This query starts by choosing the ‘Pancreatic Expression Database’ from the ‘Choose Database’ from the drop-down selection in the right panel. A ‘Choose Dataset’ drop-down selection menu will automatically appear. In this example, users will choose ‘Pancreatic Gene Expression’ data set. The next step involves choosing the appropriate filters to restrict the query in this first data set by clicking on the ‘Filters’ node on the left, expanding the filter section ‘EXPERIMENT:’, selecting ‘PDAC study—tissue’ and ‘Pancreatic ductal adenocarcinoma (PDAC)/Normal pancreas (NP)’. The overlapping CNAs are added as a second data set by clicking on the second ‘Dataset’ from the bottom of the left panel and choosing ‘Pancreatic Copy Number Alteration’ from the ‘Choose additional dataset’ drop down menu that will appear in the right panel. Clicking the ‘Results’ button on the left side of the toolbar will retrieve a result table. To generate the graphical view of the results, simply hit the UCSC or CIRCOS buttons on the right side of the toolbar. (A) Single chromosome (chr 1) view in UCSC Genome Browser. (B) Whole-genome view in CIRCOS viewer.