GEISHA: an evolving gene expression resource for the chicken embryo

Abstract

GEISHA (Gallus Expression In Situ Hybridization Analysis; http://geisha.arizona.edu) is an in situ hybridization gene expression and genomic resource for the chicken embryo. This update describes modifications that enhance its utility to users. During the past 5 years, GEISHA has undertaken a significant restructuring to more closely conform to the data organization and formatting of Model Organism Databases in other species. This has involved migrating from an entry-centric format to one that is gene-centered. Database restructuring has enabled the inclusion of data pertaining to chicken genes and proteins and their orthologs in other species. This new information is presented through an updated user interface. In situ hybridization data in mouse, frog, zebrafish and fruitfly are integrated with chicken genomic and expression information. A resource has also been developed that integrates the GEISHA interface information with the Online Mendelian Inheritance in Man human disease gene database. Finally, the Chicken Gene Nomenclature Committee database and the GEISHA database have been integrated so that they draw from the same data resources.

Figure 1.

Sample gene summary page, in this case for the gene DMBX1. Data are accessed through four tabs: ‘Genes Summary’ (shown); ‘Expression’, showing chicken ISH images and anatomical location of expression; ‘Transcript Levels’, showing quantitative mRNA expression data; and ‘Other Species Expression’, showing links to ISH expression information in fruitfly, frog, zebrafish and mouse.

Figure 2.

Expression summary page for the gene DMBX1. ISH data are organized into entries according to the source date. ISH data shown in Entry 1 were generated from an in house ISH screen (GEISHA Id: DMBX1.UApcr). Additional entries (not shown) present expression data using other probes or curated from publications. Images are organized by embryo stage. Anatomical location of expression is shown to the right of the images. Clicking on a thumbnail opens a high-resolution image.