Systematic profiling of TF mRNA embryonic expression patterns. (A) Distribution of 708 TF genes by DBD class sorted alphabetically with the number in each class in parentheses. (B) Expression profiling pipeline and downstream analysis. Four examples of previously uncharacterized TFs showing the TF gene name, an illustration of the defining DBD, an in situ image for the gene, and annotations showing primary controlled vocabulary primary annotation terms (term), the associated collapsed terms (CT), and the organ system (OS). (C) Histogram showing the density of publications per TF as shown by the number of publications recorded in FlyBase TF gene reports (x-axis) in relation to the number of TFs (y-axis). Most TFs are concentrated around the x-axis origin, that is, referenced in a small number of publications. (D) Distribution of TFs into expression classes. We classified TFs as either not expressed (Not Exp), maternally deposited only (Mat: expression for gene observed at S1-3 and may persist for the next two stage ranges), ubiquitous-only (Ubiq: gene shows only ubiquitous staining at all stages expressed, with no anatomic terms annotated), patterned-only (Pattern: gene is assigned to a tissue term at all stages expressed), patterned-and-ubiquitous (Pattern-Ubiq: gene shows ubiquitous-only staining at one or more stages and pattern annotations in others, or a pattern with a weaker ubiquitous background). (E) Fold enrichment of fraction of TF vs. all genes (7,042) at each stage-range across expression classes. Color code for expression class is as in 1D.
Hammonds et al. Genome Biology 2013 14:R140 doi:10.1186/gb-2013-14-12-r140