Data-mining the FlyAtlas online resource to identify core functional motifs across transporting epithelia

Chintapalli, V.R., Wang, J., Herzyk, P. , Davies, S.A. and Dow, J.A.T. (2013) Data-mining the FlyAtlas online resource to identify core functional motifs across transporting epithelia. BMC Genomics, 14(518), (doi:10.1186/1471-2164-14-518)

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Abstract

<p>Background Comparative analysis of tissue-specific transcriptomes is a powerful technique to uncover tissue functions. Our FlyAtlas.org provides authoritative gene expression levels for multiple tissues of Drosophila melanogaster (1). Although the main use of such resources is single gene lookup, there is the potential for powerful meta-analysis to address questions that could not easily be framed otherwise. Here, we illustrate the power of data-mining of FlyAtlas data by comparing epithelial transcriptomes to identify a core set of highly-expressed genes, across the four major epithelial tissues (salivary glands, Malpighian tubules, midgut and hindgut) of both adults and larvae.</p> <p>Method Parallel hypothesis-led and hypothesis-free approaches were adopted to identify core genes that underpin insect epithelial function. In the former, gene lists were created from transport processes identified in the literature, and their expression profiles mapped from the flyatlas.org online dataset. In the latter, gene enrichment lists were prepared for each epithelium, and genes (both transport related and unrelated) consistently enriched in transporting epithelia identified.</p> <p>Results: A key set of transport genes, comprising V-ATPases, cation exchangers, aquaporins, potassium and chloride channels, and carbonic anhydrase, was found to be highly enriched across the epithelial tissues, compared with the whole fly. Additionally, a further set of genes that had not been predicted to have epithelial roles, were co-expressed with the core transporters, extending our view of what makes a transporting epithelium work. Further insights were obtained by studying the genes uniquely overexpressed in each epithelium; for example, the salivary gland expresses lipases, the midgut organic solute transporters, the tubules specialize for purine metabolism and the hindgut overexpresses still unknown genes.</p> <p>Conclusion Taken together, these data provide a unique insight into epithelial function in this key model insect, and a framework for comparison with other species. They also provide a methodology for function-led datamining of FlyAtlas.org and other multi-tissue expression datasets.</p>

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Herzyk, Dr Pawel and Wang, Mrs Jing and Dow, Professor Julian and Davies, Professor Shireen and Chintapalli, Dr Venkateswara
Authors: Chintapalli, V.R., Wang, J., Herzyk, P., Davies, S.A., and Dow, J.A.T.
College/School:College of Medical Veterinary and Life Sciences > Institute of Molecular Cell and Systems Biology
Journal Name:BMC Genomics
Publisher:BioMed Central
ISSN:1471-2164
ISSN (Online):1471-2164
Copyright Holders:Copyright © 2013 The Authors
First Published:First published in BMC Genomics 14(518)
Publisher Policy:Reproduced under a Creative Commons License

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