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As many as 1099 genes (p-value < 0.01 and 1.5-fold-change), representing 74% and 30% of the signature genes detected with Agilent 22 and 44K pangenomic microarrays, respectively, were shown to be modulated in common in six independently performed experiments.
This is in agreement with the findings reported by Goyak et al., showing that the number of genes modulated in common in ten human hepatocyte donors treated with arochlor 1254, di 2-ethylhexyl phthalate or phenobarbital, di 2-ethylhexyl phthalatee toral deregulated genes [25].
Only a few, mainly p53-dependent, genes are modulated in common by both concentrations.
Only a few I-IUdR-responsive genes, mainly showing p53-dependent regulation, are modulated in common in the several human cell lines we tested.
In our present study, we found that only a few, mainly p53-dependent, genes like CDKN1A, GADD45A, DKK1, FHL2 are modulated in common by two various concentrations of I-IUdR.
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In this case, the differences were even higher because only 34 out 952 genes modulated in S1587-17 were common to both gene sets.
This effect is modulated in cis by another common SNP, also located within the 5′UTR, whilst a common SNP in the 3′UTR influences allelic expression independent of rs143383.
In order to assess the reliability of microarray results, we considered 9 DE genes as candidates for validation by qRT-PCR as following: 3 common genes modulated in both cell lines (PTPRO, KRT18, NDRG1), 3 genes modulated exclusively in Colo320R (ID1, WIF1 and AVEN) and 3 in HT29R (TGFB1, MDK, and CYR61) cell lines, respectively.
All the common genes were modulated in the same direction by both species, indicating they probably fulfill the same functions in defense.
Whereas about 400 genes were modulated in each age group only 184 were common to both groups and 198 and 186 genes were modulated only in the aged or in young group, respectively.
From the 207, we found that 32 spots were modulated by water stress in the wild-type plants and 62 were modulated in the mutant plants, including 25 spots that were common to both genotypes.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com