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Finally, to select for statistically significant changes, genes were designated as 'differentially expressed' if the corresponding ratios varied by at least 2-fold in at least 2 out of 56 samples (consistent with recommended criteria [67], [68]).
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Two of the most changed genes were ones involved in the detection of pheromones, the hormonelike scents with which fruit flies signal their activities.
They used GO category and MeSH term to analyze the microarray dataset and discovered that those changed genes were related with cell death, apoptosis, oxidative stress, inflammation, and neurotransmitters in the brain.
We report that a significant proportion of changed genes were found near the targeted gene.
Significantly changed genes were overrepresented in a number of pathways, most notably the cytoskeleton functional category.
For ercc1 and neb mutants, the changed genes were distributed more widely on chromosome 7 and 2 respectively.
Microarray results for significantly changed genes were confirmed by quantitative reverse transcriptase PCR (qRT-PCR) (Figure 1B).
Therefore, we asked whether the most significantly changed genes were common between the MM and MD data.
Only 15 of the 100 most significantly changed genes were similar between the experimental systems (Figure 6 and 7).
Significantly changed genes were selected with a cut-off of P < 0.05 and fold change ≥ 2.0.
Lists of significantly changed genes were similarly analyzed using Ingenuity Pathway Analysis [ 12].
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