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.