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Open Access Methodology article

SPIEDw: a searchable platform-independent expression database web tool

Gareth Williams

Author Affiliations

Wolfson Centre for Age-Related Diseases, King’s College London, London Bridge, London SE1 1UL, UK

BMC Genomics 2013, 14:765  doi:10.1186/1471-2164-14-765

Published: 7 November 2013

Abstract

Background

SPIEDw is a web tool designed to facilitate fast and simple quantitative querying of publically available gene expression data. The resource is motivated by the observation that transcriptional profiles can serve as effective means of comparing biological states across a wide set of experiments.

Results

Gene expression data for over 200,000 experiments across multiple species and platforms have been collected into a searchable database. The new resource is a development of the previously published SPIED, which was designed to be downloaded and queried locally with SPIED software. SPIEDw features three significant improvements over the original version. Firstly, the number of experiments covered has been doubled and now includes Agilent and Illumina technologies. Secondly, SPIEDw has an enhanced search algorithm for speedy web-based querying and lastly an abridged dataset comprising the most regulated genes has been included for a speedier search and searching for enrichment of gene sets.

Conclusions

SPIEDw is simple to use, not requiring any expertise in microarray analysis, and the output straightforward to interpret. It is hoped that this will open up gene expression data mining to the wider research community.

Keywords:
Global gene expression; Connectivity map; Microarray; EGF receptor; Parkinson's disease