We validated the model's capability to encompass experimentally observed phenotypes for the parent strain and derived mutants designed for significant perturbation of redox and energy pathways.
Among the chimpanzees, expected heterozygosity is highest in the central group and lowest in the western group (Table S23), and its range encompasses values observed in human populations from East Asia to the Americas.
As an example, Msh2 enters into heterodimeric complexes with Msh3 and Msh6, so it might be expected that the set of genetic interactions for msh2Δ would encompass those observed on deletion of both its partners.
However, the baseline SUXmax for this lesion was only 3.3, resulting in wide confidence limits for spurious change (−54 to 119 %), which encompass the observed % change and leads to reclassification as SMD.
In case 2, a small deletion of 10 kb on 7q34 was observed encompassing the KEL blood group gene.
In case 3, a small deletion of 10 kb on 7p22 was observed encompassing the SDK1 sphingosine dependent protein kinase gene.
Analyses of gene networks encompassing the alterations observed between young and aged prostate stroma demonstrated a significant enrichment for inflammation pathways, the NF-κB program, and collagens, among others.
Superior to Vp, a single cluster was observed encompassing the pontine reticular formation, ascending superiorly into midbrain reticular formation including much of the tegmentum including substantia nigra, ventral tegmental area and red nucleus, and tectum including quadrigeminal body and periaqueductal grey.
As shown in Table 4, deletion in the locus encompassing SEC11L3 (18q21.32) was observed to be the most recurrent alteration (13 out of 19 samples; 68%).
While the NMR p53 coding sequence is, not surprisingly, subject to purifying selection (Ka/Ks = 0.26), a window from codons 41 80 was observed, encompassing transactivation domain 2 (TADII) and most of the proline-rich domain (PRD), which had a signature of positive selection (Ka/Ks = 2.19).
