To accomplish this, we made multiple comparisons of the enriched GO terms obtained for deregulated transcripts (minimum fold change value ≥ 1.5; ANOVA t test p-value ≤ 0.05) at individual time-points.
The precursor fold-back structures have an MFE (Minimum Free Energy) ranging from -23.9 to -110.7 kcal/mol, and more than 77% had an MFEI (Minimum Fold Energy Index) value greater than 0.7 (Table 3).> -wrap-foot> aminimal folding free energy index (MFEI) was calculated according to Zhang et al. [ 99].
The minimum fold change value was set to 2. Resulting genes were classified according to their functions against the background of gene-ontology databases and the underlying literature and experimental background.
When the minimum fold change value was set at two times the standard deviation of all protein ratios in the control sample, the total number of significantly changed proteins was reduced to 629 with 364 up-regulated and 265 down-regulated (Additional file 2 Table S2).
Finally, after testing these 48 transcripts, 12 could be considered as labile transcripts with a minimum fold decrease of −2.65 log10 (value arbitrary chosen), and 11 of them could be considered as persistent transcripts with a maximum fold decrease of −1.75 log10.
The average minimum folding free energy value of the hairpin structures was −39.71 kcal/mol in P. notoginseng, which is higher than that found in Arabidopsis (−59.50 kcal/mol) [ 27].
Differential expression analysis was performed using the Bioconductor package edgeR [ 44] (minimum fold change = 4, p-value cutoff = 0.001 after FDR correction).
For the analysis, we set the minimum fold change, delta and median FDR values to 2, 0.69 and 15.8 respectively.
Among the 476 differentially expressed transcripts (identified using a minimum fold change of ±1.5 and corrected p value <0.05) 149 were expressed at higher levels in Sod2-/ erythroblasts, while 327 were down-regulated.
The statistical significance of fold-changes between Chd1-shRNA induced and uninduced samples was determined using a paired t-test, a minimum fold change of 1.4, and a delta value of 1.9 (SAM Analysis) (Tusher et al., 2001).
