Complex diseases like cancer are regulated by large, interconnected networks with many pathways affecting cell proliferation, invasion, and drug resistance.
Pharmaceutical research has increasingly relied on reductionist approaches, even though systemic diseases such as cancer and heart disease are managed by large, interconnected networks with many pathways affecting pathological signaling [4,5].
Sixteen pathways were enriched in the biggest responsive gene module identified by ClustEx, including many known pathways affected by TNF, such as Apoptosis, Notch signaling pathway, Jak-STAT signaling pathway, Toll-like receptor signaling pathway and Cell cycle (Table 1, Additional file 2).
Many pathways are affected by cancer, as recently shown for HCC.
This prompted us to investigate further the mechanism underlying p21Cip1/Waf1 up-regulation upon CTDSP2 expression, as many pathways can affect the expression of p21Cip1/Waf1 (reviewed in [ 35, 36]) and CTDSP2 is unlikely to directly regulate p21Cip1/Waf1 itself.
Not surprisingly, many obesity gene variants appear to be involved in pathways affecting energy homeostasis.
One of the difficulties with HD therapy development is the complex web of dysfunction resulting from the great many processes and pathways affected by mHtt protein in susceptible neurons.
Diseases will often result in general perturbations of homeostasis, with many general metabolic pathways affected.
We observed many factors and pathways affected by MT19c, including some related to tumor growth and survival, such as DNA damage response, apopotic genes, insulin, and PPARγ.
Because many of the pathways affected by carbonyl stress are well conserved, our observations and their underlying datasets provide a resource for future studies in yeast and other cell types.
Significant alterations in gene expression were found for all treatments and many of the gene pathways affected, most notably those associated with oxidative phosphorylation and protein synthesis, overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied.
