University of Dundee

Lamond Group upgrades its Encyclopedia of Proteome Dynamics (EPD)

18 Aug 2014

The Lamond Group has generated an important new update to its Encyclopedia of Proteome Dynamics (EPD). First launched in 2013 (Larance et. al., 2013 Mol Cell Proteomics. Mar; 12(3): 638-50) the EPD is a free to use, searchable online database that provides access to a large volume of quantitative proteomics and gene expression data characterising proteome dynamics, generated in the Lamond Laboratory at the Centre for Gene Regulation and Expression in the College of Life Sciences, University of Dundee. 

The EPD contains data from experiments that analyse multiple 'protein properties', including protein abundance, subcellular localisation, rates of protein synthesis and degradation, formation of protein complexes and variations in protein abundance and gene expression levels across the cell cycle. This includes information on the properties of separate protein isoforms and post-translationally modified forms, where available.

This significant, new update features a major redesign of the user interface as well as many backend changes to add new features, enhance speed, and greatly improve the overall user experience (http://www.peptracker.com/epd/).

The EPD provides a searchable data viewer to communicate the results from these complex, large data sets via a convenient graphical interface. Data can be searched for results obtained on a protein of interest by entering different types of 'search terms', e.g. either a Uniprot accession number, gene symbol, protein name, or a term used within Uniprot to describe protein characteristics.

Professor Angus Lamond, who heads the Laboratory for Quantitative Proteomics in the newly opened CTIR Building, said, “The EPD is central to our 'Open Data' policy and to our focus on exploring new ways to share our data as conveniently and effectively as possible with the wider biomedical research community. In 2014 we have continued to expand both the volume and range of data available within the EPD.”

This new version of the EPD was created in the Lamond group by Alejandro Brenes (a graduate of the Data Science Degree at the University of Dundee’s School of Computing) and Rob Kent, building on prior work by Yasmeen Ahmad. The EPD represents an achievement for Dundee at the forefront of proteomics data sharing.

The Lamond group plan to continually add new data sets to the EPD, derived from their ongoing experiments using both human cells and model organisms.

The EPD is part of the larger PepTracker software project in the Lamond Laboratory, which aims to create user-driven tools for improving the management, visualisation, analysis and sharing of complex, large data sets from experiments on proteomics and gene expression. http://www.peptracker.com

 

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