Genome wide expression arrays have been made possible by the annotation and gene predictions of whole genome sequence data for human and a large number of model organisms.
Within the fields of ecology and ecotoxicology, this development is particularly welcome due to the large number of model organisms, of which few have a well-characterized genome.
Xenbase is a large-scale model organism database (MOD) and community resource for researchers working with the frog species, Xenopus tropicalis and Xenopus laevis.
Therefore, elucidating the properties of the key genetic interconnections that orchestrate myogenesis in a larger set of model organisms is necessary to reveal the core myogenic circuits.
Such regions and genes constitute a challenge even for very large sequencing projects of model organisms.
In model organisms large scale studies of gene expression have identified numerous properties of genes and proteins that significantly correlate with selective constraints.
In spite of this plethora of work aimed at identifying the key TFs responsible for a phenotypic contrast of interest (e.g. healthy versus disease), experimental validation linking co-expression with co-regulation remains scarce and, by and large, available only for model organisms.
Usage of retrotransposons as alternative promoters and as a source of new lncRNA has been described for many individual examples, and also at a large global scale for model organisms such as humans, mice, and Drosophila (Peaston et al. 2004; Cohen et al. 2009; Faulkner et al. 2009; Kelley and Rinn 2012; Lenhard et al. 2012; Batut et al. 2013).
Consequently, a number of studies have attempted prediction of SL interactions in human, a majority by extrapolating SL interactions inferred through large-scale screens in model organisms.
Fine-grained yet large-scale comparisons between model organisms, especially vertebrates such as mouse or zebrafish and humans, is increasingly important.
