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A score of over 1.3 was considered to be a significant level of enrichment in the gene set with a minimum gene count threshold of ≥ 2.
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"Count" means the threshold of minimum gene counts belonging to an annotation term, and "EASE" is a modified Fisher Exact P value.
Overrepresented biological processes were selected at the threshold of Fisher Exact Test P-Value ≤ 0.05 and minimum gene counts belonging to an annotation term ≥ 2%.
Allelic frequencies were calculated by gene counting.
RNA-Seq gene counts.
The differentially expressed genes were determined after applying a minimum read count cut-off of 10, Log fold-change cutoff of 0.58 (minimum one fold-change) and RPKM value greater than 0.1.
GO analysis was performed using either DAVID analytical software for GOTERM_BP_FAT by using an EASE score <0.05 and gene set count minimum of two required for a functional pathway to be considered significant [ 30] or GOrilla where four genes were required to be considered in each annotation and a q-value cutoff <0.01 [ 31].
Dilution was appropriate to yield a minimum 100-cell count at each counting.
The minimum expected count is.06.06
The viable count is 1.07×109 cfu·greatlyexceedingeeding the minimum viable count requirement (106 cfu·g−106
This metric provides the routing minimum hop count.
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