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Given this almost six-fold difference in irradiance, it is not surprising that "Photosynthesis" was the most over-represented GO term in the comparison between field-grown and cabinet-grown Yukon plants, and the most statistically significant category in the entire GO dataset.
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A total of 3467 genes were mapped to 14 statistically significant categories (p<0.05; Table 1).
Those statistically significant categories and subcategories were shown in Figure 3C.
Statistically significant categories, either over- or underrepresented, were selected according to their corrected p-value (False Discovery Rate (FDR) ≤ 5E-2), using a hypergeometric test.
Only four genes were unique to 20% CR compared to control, with no statistically significant functional category identified.
Comparison of raw-score analysis and category analysis saw the improvement seen in Role Limitation due to Emotions (difference of means 4.4, P = 0.03 for two-tailed t-test) to be not statistically significant in Category analysis (P = 0.09).
Figure 3 lists the 30 most statistically significant annotation categories which either showed statistical enrichment in the combined analysis across all time points or at a single time point.
Using a functional enrichment analysis of genes (see supplemental files: Tables S2, S3, S4, S5, S6, S7) it was possible to individuate statistically significant functional categories that are over- or under- represented in the differentially expressed gene-lists of the efflux pump s -deleted mutant strains described in this work in respump s -deletedd-type.
The bioinformatics analysis strategy described above and in Figure 1 revealed two replicated and statistically significant GO categories.
Ingenuity Pathways Analysis (IPA 8.0, Ingenuity® Systems) was used to identify statistically significant functional categories in the data set using a modified Fisher Exact test, with P<0.05 considered significant.
Then, these selected networks were explored to identify statistically significant functional categories (p-value < 10-3) and canonical pathways (p-value < 5 10-2).
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