Search the Image Database

Search our extensive digital library database for in situ embryonic images.


Search for Co-Expressed Genes

Genomewide Expression Maps (GEMs) provide spatially aggregated levels of genome-wide expression for each pixel at a given stage and orientation. Click any GEM to begin your fine-tuned search for co-expressed genes.

% of Genes

Analyze Gene Lists

Enter a list of Drosophila melanogaster gene symbols or FlyBase FBgn accessions. Separate entries with commas, spaces, or line breaks.

Upload a list (TXT or CSV) of gene symbols or FBgn accessions.

Welcome to FlyExpress

FlyExpress is a freely accessible online knowledgebase offering users an opportunity to explore and analyze expression patterns of developmental genes in Drosophila embryogenesis. FlyExpress contains a unique digital library of over 100,000 standardized images capturing the expression of thousands of genes at different developmental stages. Use our image-matching search engine and genome-wide summaries of spatiotemporal expression patterns (GEMs) to find genes with similar and overlapping patterns of expression in the developing embryo. After you have retrieved a set of co-expressed genes, use FlyExpress’ online toolkit for discovery including new motif-finding tools (QSER and OMP) to identify novel regulatory domains and an interactive dotplot viewer to visualize common intergenic motifs between pairs of co-expressed genes.

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Download our free myFX software for Windows and Mac OS to process and analyze images depicting embryonic gene expression in the Drosophila fruitfly. It also utilizes FlyExpress resources, straight from your Desktop.

iPhone App

Download our free iFX mobile app from the iTunes App Store and search our image database on-the-fly!

Citing this Resource

Kumar S, Boccia K, McCutchan M, Ye J (2012) Exploring spatial patterns of gene expression from Fruit Fly embryogenesis on the iPhone. Bioinformatics 28:2847-2848. [Download PDF]

Konikoff C, Karr TL, McCutchan M, Newfeld SJ & Kumar S (2012) Comparison of embryonic expression within multigene families employing the FlyExpress discovery platform reveals significantly more spatial than temporal divergence. Developmental Dynamics 241:150-160. [Download PDF]

Kumar S, Konikoff C, Van Emden B, Busick C, Davis KT, Ji S, Wu L-W, Ramos H, Brody T, Panchanathan S, Ye J, Karr TL, Gerold K, McCutchan M & Newfeld SJ (2011) FlyExpress: Visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis. Bioinformatics 27:3319-3320. [Download PDF]

Copyright Notice: The images containing expression patterns in FlyExpress are protected by copyright. It is our belief that the "not-for-profit" effort to build and display this library of images is covered under the " fair-use doctrine." Therefore, although you can locate and access these images through our resource, we cannot grant you rights to reproduce them for any purpose. If you wish to reproduce them, we advise you to contact the authors of the original research publications and electronic resources to obtain the requisite permissions.