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Consistent with previous studies [24], [25], [30], [31], we found that dioxin exposure resulted in relatively low-magnitude changes in transcript levels for most affected genes.
This rat organ culture model uses cytokine exposure to induce wide gene expression changes with the most affected genes having known reported functions in disc degeneration.
Some of the most affected genes were associated with phagocytosis — the process by which immune cells take up extracellular material for clearance and degradation.
The shared genes include detoxification-related transferases, cytochrome P450 genes and enzymes with functions in nucleotide, amino acid and fatty acid metabolism, which all are among the most affected genes in our analyses.
We validated several of the most affected genes by qRT-PCR in the three larval stages and found a good correlation between the microarray and qRT-PCR results (Table 2).
Nevertheless, ND4 and ND6 were still the most affected genes.
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Taking the 200 most significantly affected genes, we grouped them in (i) genes more activated in BRL3ox under drought compared to WT (Supplementary Data 10) and (ii) genes more repressed in BRL3ox under drought compared to WT (Supplementary Data 11).
Among the VD-deficiency altered-gene list, we found Neuronal PAS domain 2 (NPand) and Period Homolog 2 (Per2) as the most significantly affected genes by vitamin D deficiency in the peri-implant tissue (Table 1).
The most frequently affected genes included TP53, APC, and BRCA2.
Among the most dramatically affected genes were those included in the cellular response to oxidative stress.
These tools enable users to view the most commonly affected genes or pathways in one or more cancer projects.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com