FlyAtlas: a comprehensive online atlas of gene expression in Drosophila

Lead Research Organisation: University of Glasgow
Department Name: School of Life Sciences

Abstract

Multicellular organisms, from humans to flies to plants, have distinct tissues specialized for distinct tasks. What makes one tissue different from another? Every cell in the body contains the same genetic code (of 15000-25000 genes, depending on the organism); but different tissues switch on (express) different subsets of these genes. For example, skin is skin because it expresses keratin, and liver is liver because it expresses detoxifying enzymes. To understand how organisms work, therefore, we need to know which genes are expressed in which tissues. There are many techniques for mapping gene expression levels, but most are laborious and prone to error. By contrast, DNA microarrays allow the relatively precise measurement of expression levels of all genes in a genome in a SINGLE experiment. A comprehensive, microarray-based 'atlas' of gene expression in specific tissues and cell types thoughout an organism is thus a fantastically useful resource to a whole community; if the job is done properly, there is no need to do it again. This proposal is to extend such a service for the Drosophila (fruit fly) research community, both in the UK and worldwide. A pilot project (with 9 adult tissues) has attracted over two thousand users in its first 6 months, confirming the need for such a resource. We propose to extend the resource to further tissues and further life stages, with the data easily accessible on the web (at flyatlas.org). The resource will allow scientists to target their effort more precisely, saving money and time, and reducing unnecessary animal use.

Technical Summary

The Drosophila research community is large, fast-moving, and has contributed greatly to our understanding of organismal function, from development to behaviour. With the publication of the Drosophila genome project, it has become clear that, for at least half the 13500 or so genes, there is no known function. A reverse genetic strategy in a simple organism like Drosophila is clearly a potent tool for elucidating gene function - but what phenotypes should be studied? Clearly, the answer depends on the tissues in which a gene is expressed. Rather than leave post-docs worldwide labouring with Northerns, RT-PCRs or in situs of variable quality and comprehensiveness, it would make sense to do the job once, properly. Flyatlas (flyatlas.org) puts experimenters in touch with their tissues quickly, clearly and unambiguously. The original dataset, generated through BBSRC IGF funding, comprises 9 adult tissues, two larval tissues, and a whole-fly sample. It is based on Affymetrix Dros2 chips, with 18770 probesets to cover 13500 genes, and so is accurate and comprehensive. Since its launch in the autumn of 2006, it has attracted over a thousand users, confirming the hunger of the community for such data. This proposal is to extend the dataset to further adult tissues and further life stages, to provide a one-stop lookup-shop for Drosophila expression, and a rich bioinformatic resource for novel meta-analysis.

Publications

10 25 50

publication icon
Dow JA (2010) Drosophila provides rapid modeling of renal development, function, and disease. in American journal of physiology. Renal physiology

publication icon
Dow JA (2009) Insights into the Malpighian tubule from functional genomics. in The Journal of experimental biology

publication icon
Hirata T (2012) Ion and solute transport by Prestin in Drosophila and Anopheles. in Journal of insect physiology

publication icon
Stergiopoulos K (2009) Salty dog , an SLC5 symporter, modulates Drosophila response to salt stress in Physiological Genomics

 
Description This grant produced an online resource, flyatlas.org, which maps out expression patterns of all Drosophila genes across multiple tissues and multiple life stages.

We have data-mined the resource for several significant papers; but most significantly, our resource has been cited a thousand times by other users worldwide. (See https://scholar.google.co.uk/scholar?cites=13302169808576348992&as_sdt=2005?iodt=0,5&hl=en). This BBR funded grant thus did exactly what it said, and perhaps the key finding was that the hunger for such functional genomic data was far greater than anyone had predicted.
Exploitation Route As evidenced by the citation record for FlyAtlas, the dataset has been put to use in fields far more diverse than just Drosophila genetics.
Sectors Agriculture, Food and Drink,Healthcare,Pharmaceuticals and Medical Biotechnology

URL http://flyatlas.org
 
Description These datasets led to funded contract research, CASE awards anda BBSRC IPA award with Zoetis and with BASF.
First Year Of Impact 2009
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description NIH Centre grant
Amount $400,000 (USD)
Funding ID DK100227 
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 03/2013 
End 03/2018
 
Description Collaboration with BASF 
Organisation BASF
Country Germany 
Sector Private 
PI Contribution Based on our leading position in insect biology and functional genomics, we have had longstanding collaborations with BASF in RTP, North Carolina. We have performed extensive contract research over 5 years, and continued to discuss possibilities for the development of new targets. We have also tested novel compounds from BASF against in-house assays.
Collaborator Contribution BASF have funded extensive periods of contract research with our group, and paid us for consultancy when testing novel compounds. They have also hosted a FLIP award with our group, led by Professor SHireen Davies, giving us access to leaders in several of the key chemistry, mode-of-action and regulatory groups in North Carolina. This has informed our plans to develop a spin-out from our research.
Impact Large gene expression datasets and fly lines developed. Details are confidential.