However, only six genes had fold changes higher than 1.5, which was chosen as the minimal fold change relevant to report.
First, the data was filtered for baseline average raw signal intensity of at least 200, followed by filtering for a minimal fold change difference of 1.5.
Of these, 67 genes were up-regulated and 73 were down-regulated with a minimal fold change of ±1.41 (log2 ratio ≥±0.5).
Three criteria were used to determine statistically significant differential expression of genes in pigs between CS-fed and MS-fed group: (1) statistical significance: P value as determined by t test≤0.05; (2) reliability: a spot quality flag P ("P", a quality flag assigned by the software package); (3) relevance: a minimal fold change between the means of the two groups>1.1.
Because fold changes are not necessarily related to biological relevance [ 68, 69], a minimal fold change criterion was not applied.
To enrich for biologically relevant changes, only probe sets with a minimal fold change of 1.5 were selected.
Specifically, the model used for in vitro was second order polynomial model with fold change of one (that was the minimal fold change of interest in our analysis).
A minimal fold change criterion was not applied for the identification of differentially expressed genes, as fold changes are not necessarily related to biological relevance [ 90, 91].
In the present analysis, where a difference is represented by the minimal fold change, 1.10 was used as an arbitrary cut-off point.
Several additional growth factors and growth factor receptors (FGFRL1, GDF5, GDF6, IGF2R, IGFBP5) demonstrated a significant change in steady state mRNA levels (p < 0.01), but with only minimal fold change differences between neonatal and adult samples (Table 5).
