Abstract
An in situ hybridization (ISH) study was performed on 2000 murine genes representing around 10% of the protein-coding genes present in the mouse genome using data generated by the EURExpress consortium. This study was carried out in 25 tissues of late gestation embryos (E14.5), with a special emphasis on the developing ear and on five distinct developing sensory organs, including the cochlea, the vestibular receptors, the sensory retina, the olfactory organ, and the vibrissae follicles. The results obtained from an analysis of more than 11,000 micrographs have been integrated in a newly developed knowledgebase, called ImAnno. In addition to managing the multilevel micrograph annotations performed by human experts, ImAnno provides public access to various integrated databases and tools. Thus, it facilitates the analysis of complex ISH gene expression patterns, as well as functional annotation and interaction of gene sets. It also provides direct links to human pathways and diseases. Hierarchical clustering of expression patterns in the 25 tissues revealed three main branches corresponding to tissues with common functions and/or embryonic origins. To illustrate the integrative power of ImAnno, we explored the expression, function and disease traits of the sensory epithelia of the five presumptive sensory organs. The study identified 623 genes (out of 2000) concomitantly expressed in the five embryonic epithelia, among which many (∼12%) were involved in human disorders. Finally, various multilevel interaction networks were characterized, highlighting differential functional enrichments of directly or indirectly interacting genes. These analyses exemplify an under-represention of "sensory" functions in the sensory gene set suggests that E14.5 is a pivotal stage between the developmental stage and the functional phase that will be fully reached only after birth.
Highlights
One of the main challenges of developmental biology is to decipher the interplay between specific pathways and gene networks involved in the different phases of the ontogenesis of an organism
An in situ hybridization (ISH) study was performed on 2000 murine genes representing around 10% of the protein-coding genes present in the mouse genome using data generated by the EURExpress consortium
Designed to facilitate the detailed and integrated analysis of complex organs, notably the ear, ImAnno is being used for other large scale annotation projects for instance, in the developing mouse eye and teeth or the human eye fundus project
Summary
One of the main challenges of developmental biology is to decipher the interplay between specific pathways and gene networks involved in the different phases of the ontogenesis of an organism. Genepaint.org; http://www.eurexpress.org) aim to develop a powerful mouse transcriptome digital atlas, by means of in situ hybridization (ISH) in the whole animal at a specific stage of development: embryonic day 14.5. In this context, as members of the consortia, we were responsible for producing a subset of in situ hybridization slides, as well as the corresponding micro-photographs, via an automated microscopy image acquisition system. Using the existing ISH plates, this led to 11,000 additional ISH micrographs with higher magnification focused on detailed analysis of 25 ear and sensory system tissues or structures of late gestation embryos (E14.5)
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