Advances in the FlyExpress Platform Facilitate the Integration of Gene Expression Spatial Patterns with Associated Regulatory Sequence. Michael E. McCutchan¹, Sudhir Kumar^1,2. 1) Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State Univ, Tempe, AZ; 2) School of Life Sciences, Arizona State Univ, Tempe, AZ.

   The overarching goal of the FlyExpress project is to develop computational methods and practical bioinformatics resources for data-driven integrative analyses of expression pattern images and sequence data to discover functional, genetic, and regulatory interactions among genes and genomic elements. FlyExpress contains a large dataset of spatial expression patterns from high throughput studies and from peer-reviewed journal articles. We enriched the existing data by standardizing and annotating images such that they are aligned and contain information on developmental stage and anatomical view. From these data scientists can now visualize temporal sequences of gene expression (Time-course embryos) for individual genes, informative global views of stage- and view-specific expression patterns (Genomewide-Expression-maps, GEMs), and search for co-expressed genes via spatial expression pattern matching. We have now evolved the FlyExpress platform by adding new functions. First, genome sequence data is now integrated with results from expression pattern studies, such that researchers are able to explore common motifs found in the genomic region of a query image and thus identify candidate trans-acting regulators of that images gene expression pattern. In refined stage-based image searches for matching expression patterns and for time-course based embryonic gene expression displays, we employ our new automated within stage predictions that affords a more biologically grounded basis for proposing a set of co-expressed genes. In addition, a new sketch-and-find utility enables researchers to paint desired patterns on selected GEMs to identify all co-expressed genes in those locations. The updated FlyExpress platform can be accessed at http://www.flyexpress.net .