There is a clear alignment and separation of developmental stages along the PC1 in the plot (Additional File 1).
We next sought to determine whether orthologous CRMs could be identified through alignment of noncoding regions surrounding developmental genes of interest.
Analysis of data set overlap (Additional file 10) revealed that about 47% of the total DE genes (501/1075) were expressed in both the wild-type and the mutant (commonly shared expression), which supports the developmental alignment of the two clones.
To examine alignment of timing switching domains to developmental domains, replication timing data from 9 cell types (ESC/iPSC, EBM3/EPL, EBM6/EpiSC, NPC, Mesoderm, Endoderm, partial iPSC, MEF, and Myoblast) were assembled from the ReplicationDomain.org database [ 44] and plotted together with the data from BAF250a mock and OHT.
We note that in this comparison our main limitation was alignment of the apple and tomato developmental time courses where in tomato the ethylene burst occurs at the breaker stage (42 DAP, days after pollination in cv. Ailsa Craig), while in apple this is a post-harvest phenomena.
From this point of view, the concept of developmental space is also in alignment with Maslow's hierarchy of human needs.
Because of this spatial alignment, abnormalities in developmental processes or in clearance of damaged, particularly insoluble proteins, are often observed in vivo as localized opacities or cataracts.
Cancer: A Problem of Developmental Biology.
Laboratory of Developmental Biology, Royal Victoria Hospital, McGill University Health Center, McGill University, Montreal, Quebec, Canada.
