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Overall, we conclude that this novel LRH-1 pathwaythway represents a core pathway that is required for hepatic ER stress resolution.
Atg12 is part of two protein conjugation systems, each composed of two ubiquitin-like proteins (Atg8 and Atg12) and three enzymes (Atg3, Atg7 and Atg10 shown in Figure 9, the core pathway) that are required for their conjugation reactions.
It is interesting that the central part of glycolysis (00010), the Embden-Meyerhof pathway, is partially conserved among Gammaproteobacteria (Fig. 2d), whereas the core pathway that comprises the tricarbon compounds is widely functionally conserved among the analyzed organisms, including the oxidation of pyruvate to acetyl CoA.
More generally, as blockade of autophagy in fibrogenic cells from different organs also attenuates fibrogenesis, it appears that autophagy is an evolutionarily conserved, core pathway that contributes to, and regulates, the fibrotic response in a wide range of tissues.
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In particular, core pathways that attenuate pathologic protein aggregation are remodeled, including small heat shock proteins and components of cytosolic HSP70/HSP90 chaperoning pathways.
The statistically significant enriched biological pathways (p-value < 0.05) are considered as potential core pathways that contribute to the survival or reproduction of a phenotype.
We also provide a network view of disrupted pathways to show how copy number alteration can disrupt core pathways that are essential for cancer development and progression.
However, detailed genetic analyses have unraveled the pivotal mechanisms controlling pancreatic carcinogenesis, and cluster analysis of recurrently mutated genes has defined twelve different core pathways that lead to aberrant signaling in PDAC cells [ 12].
Studying the interaction and crosstalk of genomic information exchange between the epigenomic, genomic and proteomic space may assist in identifying core pathways that are continuously dysregulated, starting from epigenome to proteome.
The finding that there were no apparent variations in the abundance of genes for the core metabolic pathways in spite of the decrease in taxonomic diversity (Fig. 3A) might have been due to the functional redundancy of the genes for these common core pathways that were shared by the soil microbial members at Week 0 and the members at the weeks after the pollution.
Moreover, although they demonstrated that there are several core pathways that are recurrently targeted in most pancreatic cancers, such as those that control cell division, cell death, adhesion, and various signaling pathways [ 16], the pathway components that were altered in any individual tumor varied widely.
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