CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies

doi:10.1186/1471-2105-7-418

BMC Bioinformatics

Volume 7

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CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies

Jussi Paananen¹^,2 , Markus Storvik³ and Garry Wong¹^,3

¹Department of Neurobiology, A. I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, 70211 Kuopio, Finland

²Department of Computer Science, University of Kuopio, P.O. Box 1627, 70211 Kuopio, Finland

³Department of Biochemistry, University of Kuopio, P.O. Box 1627, 70211 Kuopio, Finland

author email corresponding author email

BMC Bioinformatics 2006, 7:418doi:10.1186/1471-2105-7-418


Published:	22 September 2006

Abstract

Background

Current genomic research methods provide researchers with enormous amounts of data. Combining data from different high-throughput research technologies commonly available in biological databases can lead to novel findings and increase research efficiency. However, combining data from different heterogeneous sources is often a very arduous task. These sources can be different microarray technology platforms, genomic databases, or experiments performed on various species. Our aim was to develop a software program that could facilitate the combining of data from heterogeneous sources, and thus allow researchers to perform genomic cross-platform/cross-species studies and to use existing experimental data for compendium studies.

Results

We have developed a web-based software resource, called CROPPER that uses the latest genomic information concerning different data identifiers and orthologous genes from the Ensembl database. CROPPER can be used to combine genomic data from different heterogeneous sources, allowing researchers to perform cross-platform/cross-species compendium studies without the need for complex computational tools or the requirement of setting up one's own in-house database. We also present an example of a simple cross-platform/cross-species compendium study based on publicly available Parkinson's disease data derived from different sources.

Conclusion

CROPPER is a user-friendly and freely available web-based software resource that can be successfully used for cross-species/cross-platform compendium studies.