Fig. 2
Differential expression analysis of proteins in brains of 5xFAD mice. a Volcano plots depicting the protein expression logarithmic fold-changes (log10 fold-change, x-axis) and the adjusted p-values (− log10 p-value, y-axis). Differentially Expressed proteins across all time points (Age 2, 5, and 8) in cortex and hippocampus were analyzed (DE.cortex.Age2, DE.cortex.Age5 and DE.cortex.Age8; DE.hippo.Age2, DE.hippo.Age5 and DE.hippo.Age8). All proteins highlighted in blue have significantly altered expression. The candidate AD biomarker Arl8b, marked in red, is significantly upregulated in hippocampus. Gene names for potential proteins of interest with highly significant fold-changes are indicated. Proteins not significantly changed in their abundance are highlighted in gray. Significance was determined using a two-tailed t-test and a Benjamini–Hochberg False Discovery Rate (FDR) set to 5%. b Numbers of differentially expressed proteins obtained by comparing the protein expression measurements of 5xFAD mice at different ages with their corresponding, age-matched, wild-type controls in cortex and hippocampus. The identifiers of the amounts of proteins analyzed were denoted analogously as in panel a. Bars indicate the numbers of significant down- (blue) and upregulated (red) proteins. c Numbers of proteins significantly differentially regulated. A2TC (Age 2, Tissue Cortex), A5TC and A8TC label the numbers of proteins for which the transgene effect is significant in cortex, at 2, 5, and 8 months, respectively. Proteins more abundant in 5xFAD mice are shown in red, while proteins more abundant in wild-type mice are shown in blue. A2TH (Age 2, Tissue Hippocampus), A5TH, and A8TH label the same comparison in hippocampus. A52TC (Age 5 vs 2, Tissue Cortex), A85TC and A82TC refer to the numbers of proteins for which the transgene effect is significantly different at two time points (5 vs 2, 8 vs 5, and 8 vs 2 months) in cortex. The numbers of proteins which increase in abundance with age are shown in red, while the numbers of proteins that decrease with age are shown in blue. The corresponding labelling for the hippocampus samples are A52TH (Age 5 vs 2, Tissue Hippocampus), A85TH and A82TH. Finally, A2THC (Age 2, Tissue Hippocampus vs Cortex), A5THC and A8THC report the numbers of proteins for which the transgene effect is significantly different in cortex and hippocampus at 2, 5, and 8 months, respectively. Higher hippocampus abundance is shown in red on the right, and higher cortex abundance in blue on the left. The underlying data are available as Additional file 3: Supplementary Excel File 1c. d–f Venn diagrams showing the numbers of total (d), downregulated (e), and upregulated (f) proteins in cortex and hippocampus, including only significantly differentially expressed proteins (DEPs). The amounts of DEPs were denoted analogously to panel c but were combined across all time points (months 2, 5, and 8); the combination of DEPs is indicated by the x (e.g., AxTC). g Correlation analysis of DEPs for A2TC, A8TC, A2TH, A5TH, and A8TH. The degree of correlation was assessed by Spearman correlation coefficients (rS) and corresponding FDR-adjusted p-values (**, p < 0.01; ***, p < 0.001). Crosses indicate no correlation. The colors denote the values of the Spearman correlation coefficients. h Example Spearman inverse correlation of A2TC versus A8TC also shown in panel g. Time-dependent changes in the abundance of 8 mitochondrial proteins (i) and transcripts (j) that play a key role in oxidative phosphorylation and ATP production. The temporal changes of the LFCs across all ages (2, 5, and 8 months) in cortex (orange) and hippocampus (blue) are shown. The statistical significance of the differentially expressed proteins and transcripts was measured with a two-tailed t-test, adjusted by the Benjamini–Hochberg multiple testing correction (*, p < 0.05, **, p < 0.01; ***, p < 0.001). All analyses are based on mean values of measured intensities from five biological replicates of tg mice per age and tissue (n = 5)