FlyExpress 7: An Integrated Discovery Platform To Study Coexpressed Genes Usingin SituHybridization Images inDrosophila

Abstract

Gene expression patterns assayed across development can offer key clues about a gene’s function and regulatory role. Drosophila melanogaster is ideal for such investigations as multiple individual and high-throughput efforts have captured the spatiotemporal patterns of thousands of embryonic expressed genes in the form of in situ images. FlyExpress (www.flyexpress.net), a knowledgebase based on a massive and unique digital library of standardized images and a simple search engine to find coexpressed genes, was created to facilitate the analytical and visual mining of these patterns. Here, we introduce the next generation of FlyExpress resources to facilitate the integrative analysis of sequence data and spatiotemporal patterns of expression from images. FlyExpress 7 now includes over 100,000 standardized in situ images and implements a more efficient, user-defined search algorithm to identify coexpressed genes via Genomewide Expression Maps (GEMs). Shared motifs found in the upstream 5′ regions of any pair of coexpressed genes can be visualized in an interactive dotplot. Additional webtools and link-outs to assist in the downstream validation of candidate motifs are also provided. Together, FlyExpress 7 represents our largest effort yet to accelerate discovery via the development and dispersal of new webtools that allow researchers to perform data-driven analyses of coexpression (image) and genomic (sequence) data.

In locusanalysis of patterning evolution in the BMPR2 Wishful thinking

“…One way to identify common mechanisms of gene regulation is to search for overlapping spatiotemporal expression domains (Konikoff et al, 2012;Kumar et al, 2017). In D. melanogaster, the anterior domain of the follicular epithelium is patterned by BMP signaling (Twombly et al, 1996).…”

Museum of Spatial Transcriptomics

“…Second, current era data has not yet been integrated into comprehensive databases. Prequel databases such as GXD, e-Mouse Atlas and Gene Expression (EMAGE) [148], and FlyExpress [149] include data from multiple sources and can be queried by gene symbol and developmental and spatial ontologies. In addition, ABA [30], EMAGE, and FlyExpress aligned ISH images to common coordinates and can be queried with expression patterns.…”