ResourcesDownloads of datasets and software
Gene expression atlases
We gather cellular resolution data on gene expression in Drosophila blastoderm embryos, and convert this data into gene expression atlases where measurements for many genes are present in the same average morphological framework. These data are especially useful for challenging computational models of gene expression. The methods are described in Luengo Hendriks et al., 2006; Fowlkes et al., 2008; Fowlkes et al., 2011; and Wunderlich et al., 2014, as well as on the website of the Berkeley Drosophila Transcription Network Project, where these methods were developed.
Links to specific datasets are below.
The wildtype Drosophila melanogaster atlas can be downloaded from the Berkeley Drosophila Transcription Network Project.
We make use of a variety of custom software for visualizing and analyzing our data. These packages are all freely available as described below.
The PointcloudToolBox is a set of MATLAB tools for analyzing pointcloud and atlas files, developed by the BDTNP.Download PointCloudToolbox from BDTNP
In collaboration with Miriah Meyer, we built MulteeSum, an interactive software package to visualize comparison of cellular gene expression profiles, described in Meyer et al., 2011. You can download the software below, preconfigured to browse the figures from Fowlkes et al., 2011. Usage instructions can be found here.Download MulteeSum
Also in collaboration with Miriah, we are currently developing a browser to visualize transcription factor binding sites, a seemingly simple, but visually complicated problem. The first version of the tool can be downloaded below.Download InSite