Listed for each of the 8,786 E. tenella genes are the normalised counts calculated by DESeq in each of the three developmental stages (gametocytes, merozoites and sporozoites), along with the calculated differential expression in gametocytes over either merozoites or sporozoites.
Relative exon expression was computed for each gene with at least two exons represented, and utilised all exons representing a given gene as r=(e− g)/ g, where e is the normalised log2 exon expression and g is the normalised log2 expression of the gene.
The comparative threshold cycle (CT) method was used for the calculation of fold overexpression where relative amount=2−ΔΔ C T, where −ΔΔ CT is the normalised signal level (threshold cycle test gene−threshold cycle endogenous control (GAPDH)) in the sample relative to the normalised signal level in the corresponding calibrator sample.
Red dots are normalised gene expression values, box plots represent median and standard deviation of the data.
Z score was compared to normalised gene expression using Pearson correlation coefficient.
Partial correlation analysis, as described elsewhere (Bailey, 1995), was applied to the normalised TF gene expression data using Spearman correlation.
In grapevines, transcriptional patterns of VIT_16s0100g00290 (SDH Class II, LIDH) and VIT_16s0100g00300 (SDH Class I, SDH) were analysed using the normalised grapevine gene expression atlas of the 'Corvina' cultivar [ 81].
Mal d 1.01 was the most expressed gene, with a normalised expression of approximately 60 A.U. in the fruit peel of 'Florina'Florina
Each average Δ CT was also subtracted from that of a calibrator (average Δ CT value of all the normal samples which provide the physiological expression of each gene target) to give the ΔΔ CT value, that is, normalised target gene expression in the different groups relative to normal.
Average GAPDH CT value was subtracted from that of each target gene to obtain a Δ CT value, that is, normalised target gene expression relative to GAPDH.
