Figure 3.

The Gene Expression Data Query Form features two search tabs: Standard and Differential Expression. The Standard Search, shown here, enables queries for expression data using one or more parameters. The Genes section allows users to find expression data for a specific gene or for a set of genes based on their function [as defined by Gene Ontology terms (Gene Ontology Consortium, 2010)], their association with mouse phenotypes [as defined by Mammalian Phenotype Ontology terms (Smith et al., 2012)], or their association with human diseases [as defined by Online Mendelian Inheritance in Man (OMIM) terms (Amberger et al., 2011)]. In the anatomical/stage section, one can search for expression data in specific anatomical structures and/or developmental stages, and one can specify whether (1) all results should be returned or only those where expression was (2) detected (i.e. present) or (3) not detected (i.e. absent). Anatomical searches combine word searching and hierarchical searching. For example, a search for expression in “diencephalon” would return expression annotations for all anatomical structures that have “diencephalon” as part of their name as well as for all their anatomical substructures such as “thalamus”. In the mutant/wild type section one can limit the searches to expression data from wild-type mice or search for gene expression in specific mutants. The Assay types section allows selection of expression data types. Auto-fill utilities help to find appropriate search terms. The illustrated search asks for ‘transcription factor binding’ genes ‘detected’ in the ‘diencephalon’ at ‘Theiler stages 17, 18, or 19’. The corresponding search results page is shown in Fig. 4. The Differential Expression Search (not shown) allows searching for genes that are expressed in some anatomical structures but not others and/or at some developmental stages but not others.