1121 genes were predicted to function in the same pathways as those examined in our study.
Clustering identified potential groups of genes operating in the same pathways, processes or molecular complexes.
The genes in the same group could be considered as being in the same pathways or involved in the same biological processes.
Several studies indicate that mRNAs in the same pathways share similar decay kinetics and could share overlapping stability control pathways [18].
However, by finding several effects in the same pathways, using even an alpha level of 0.05 for significance, we were able to identify those pathways of the greatest importance in our data set, and reinforced the overall findings.
The most important finding was that pioglitazone increased the expression of genes representing OXPHOS and ribosomal protein biosynthesis, and that this effect corrected preexisting downregulation of genes in the same pathways.
PVT1 is a c-Myc activator implicated in murine tumors and in the same pathways as c-Myc [32] and c-Myc is a transcriptional regulator affecting cellular processes such as growth, metabolism, division and apoptosis.
These additional mutations can be embedded in the same pathways and cellular processes as the gene conferring drug resistance or more changes in the same gene and may indirectly modulate the response level to the selecting drug.
Nevertheless, available studies using biopsy specimens from patients with Barrett's esophagus support a carcinogenetic role for alterations in the same pathways that caused transformation of our non-neoplastic Barrett's epithelial cells in vitro, i.e. the p16/Rb and p53 checkpoint arrest pathways, the mitogenic Ras signaling pathway, and the telomerase-dependent replicative senescence pathway.
However, analyses at the genetic network level also showed that several gwas-genes specific for single pathologies converged at the interactome level, meaning that, although the primary events may differ, the resulting functional cascades may come together and lead to alterations in the same pathways.
Because factors involved in the same pathways are sometimes able to compensate for one another when overexpressed [50] we considered the possibility that the Bur complex and CUS2 acted in the same pathway such that deletion of one gene masked the phenotype associated with deletion of the other.
