Correlation between protein and corresponding mRNA abundances
Kidney protein and mRNA expression levels had a low level of overall correlation and were also poorly correlated for significantly regulated proteins. Overall, plotting log2 transformed mRNA FC against protein FC resulted in an R2 value of 0.0061, which indicates lack of any measurable correlation (Figure 3A). The main reason for this result is the almost complete absence of significant regulation of kidney mRNAs during BW acclimation (see previous paragraph). Plotting all significantly up-regulated and down-regulated proteins against the FC of their corresponding mRNA transcripts resulted in a slightly higher R2 value of 0.185, although this correlation is still weak (Figure 3B). Few of the mRNA transcripts corresponding to significantly regulated proteins had fold changes which met the 1.85 FC threshold. These included two upregulated mRNAs, major facilitator superfamily domain-containing protein 4A (MFSD4A) andmyo -inositol-3-phosphate synthase 1 (MIPS1), and two downregulated mRNAs, myo -inositol oxygenase (MIOX) and dehydrogenase/reductase SDR family member 11 isoform X2 (DHRS11-X2). Despite meeting the FC threshold, none of these four transcripts were statistically significantly different between BW and FW fish and none of the significantly regulated mRNAs matched to genes that are represented as proteins in the DIA assay library.