Full Range: fold change between the most extreme pair of samples.
GO enrichment analysis was carried out using the gene score resampling method in ErmineJ (v3.0.2) [ 25], with full resampling of fold change used as gene scores.
Based on the full gene list (Log2 fold change ≥2/≤ - 2; FDR < 0.05) (Table 2 and Additional file 3: Table S3), we ranked genes according to the magnitude of their fold changes, regardless of whether they were up- or down-regulated.
Mutant 331Δ receptors show increased pEC50 values (∼2 4 fold change from full length) hereby showing potency similar to full length WT.
Using a p value cutoff of p < 0.05 (see methods for full statistical analysis) and a fold change cutoff of 1.85, at one hour following formoterol administration, 23 probes were significantly altered and 112 probes were significantly altered at four hours.
Full details in gene name, function, accession number, fold change and p-value for all transcripts differentially expressed are provided as an additional file (Additional file 1).
The full list of genes showing at least 1.5 fold change in expression following drug treatment in either parental or resistant cells can be found in Additional file 1: Table S1.
Figure 2 shows the total number of transcripts that are differentially expressed (fold change ≥2) in the two species at 12 and 24 hpi (full list provided in Additional file 6).
The symbols of the modulated genes are specified in the text (fold change [FC] values between brackets), while their full names are given in Additional file 1.
In total 22 genes were identified showing both significantly altered transcription and methylation (> 1.5 fold change) in zebrafish HCC (Table 2, A full list of the 194 genes investigated is presented in Additional file 8, Table S1).
This included the degradative enzymes adamts20, pxdn, nas14, and cpb and transporters slc and aqp-9, as well as genes with low fold change (e.g., hspb1, kcnab2, txlnb, kmo; see Table S1 for full names).
