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To identify genes regulated by nitrogen, water stress, and their interaction, entities were first filtered based on a fold change above 2 in at least one of the comparisons described in Table 3.
Method I was able to assign genotypes for 93 95% of B>M probes in both RILs and was unaffected by the use of filtering based on a fold change (Table 1).
A further cut-off threshold was applied based on a fold change of 2.0 between infected and control pigs.
Differentially expressed genes were selected based on a fold change between mutant and WT of at least 1.4-fold and an adjusted P-value <0.05.
The WHO criteria for reporting NI assay data are based on a fold increase in the IC50 value of a test virus compared with that of a control or reference virus (or median) IC50 value (18 ).
To identify genes regulated by nitrogen, entities were filtered based on a fold change above 2 between the two conditions: optimal nitrogen-optimal water and limiting nitrogen-optimal water.
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The first published studies for gene expression analysis selected differentially expressed genes based on a fold-change criteria between a treatment and control condition [ 48].
A diagram showing the comparisons used to sort the data is shown in Figure 4. Transcripts of interest were selected based on a fold-expression difference cutoff and a statistical strength cutoff.
In both cases, a typical analysis procedure is first to normalize experimental and batch differences between samples and then to identify up- and downregulated genes based on a fold-change level when comparing across samples, such as between a healthy and a non-healthy tissue.
TheseSET proteins are based on a common fold that appears unique to this family.
Putative transcription factor binding sites were identified in each network based on a >2 fold enrichment (yes set versus no set) and on a P-value from a one-tailed Fisher's exact test >0.05 (Fig 5).
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