Table 1.
Differentially-expressed proteins in 42 week-old CVN-AD versus WT mice.*
| Protein Name | Protein Description | Fold Change | ANOVA P-value | Cohen’s d | # Peptides | AD Association | Ms Model Proteomics | Human AD Proteomics |
|---|---|---|---|---|---|---|---|---|
| C1QB | Complement C1q subcomponent subunit B | 3.9 | 6.15E-04 | 14.25 | 1 | 26, 94, 95 | 26 | - |
| C1QC | Complement C1q subcomponent subunit C | 3.6 | 0.001 | 4.50 | 1 | 26, 94, 95 | 26 | - |
| APOE | Apolipoprotein E | 2.6 | 0.01 | 9.79 | 19 | 26, 34, 35 | 26 | - |
| GFAP | Glial fibrillary acidic protein | 2.4 | 0.039 | 10.30 | 48 | 26–28, 32–34 | 26, 27 | 28 |
| CH047 | Uncharacterized protein C8orf47 homolog | 2.4 | 0.04 | 3.31 | 2 | - | - | - |
| PP2BC | Serine/threonine-protein phosphatase 2B catalytic subunit gamma | 1.9 | 0.019 | 2.93 | 2 | 96 | - | - |
| DYN2 | Dynamin-2 | 1.9 | 1.38E-09 | 5.24 | 5 | 97, 98 | 98 | - |
| MRP6 | Multidrug resistance-associated protein 6 | 1.8 | 0.028 | 3.79 | 2 | - | - | - |
| RAB43 | Ras-related protein Rab-43 | 1.7 | 0.005 | 4.08 | 5 | - | - | - |
| UK114 | Ribonuclease UK114 | 1.7 | 4.34E-04 | 4.58 | 4 | - | - | - |
| PRDX6 | Peroxiredoxin-6 | 1.5 | 0.009 | 5.96 | 24 | 26 | 26 | - |
| LYST | Lysosomal-trafficking regulator | 1.5 | 0.042 | 1.91 | 2 | - | - | - |
| GLOD 4 | Isoform 3 of Glyoxalase domain-containing protein 4 | 1.3 | <1.00E-06 | 2.48 | 10 | - | - | - |
| AMPL | Isoform 2 of Cytosol aminopeptidase | 1.3 | 0.04 | 2.23 | 6 | - | - | - |
| LXN | Latexin | 1.2 | 0.044 | 1.71 | 3 | - | - | - |
| ENPL | Endoplasmin | 1.2 | 1.16E-05 | 1.88 | 18 | 99, 100 | - | - |
| PRDX3 | Thioredoxin-dependent peroxide reductase | 1.2 | 0.014 | 1.83 | 11 | 101 | - | - |
| SIRT2 | NAD-dependent deacetylase sirtuin-2 | −1.2 | 4.12E-06 | 1.79 | 18 | 102, 103 | - | - |
| AINX | Alpha-internexin | −1.2 | <1.00E-06 | 1.85 | 53 | 104 | 104 | - |
| MOG | Myelin-oligodendrocyte glycoprotein | −1.2 | 0.028 | 2.54 | 10 | - | - | - |
| NIN | Ninein | −1.8 | 2.02E-13 | 3.28 | 2 | - | - | - |
Differentially expressed proteins are listed with references citing previously published AD-associations, as well as references of differential expression in AD model and human AD proteomic studies. Determination of significance was made by using an ANOVA p-value <0.05 and a Cohen’s d effect size > 1.7. To compensate for the low number of replicates, an intensity-based error was used in the calculation of effect size (Supplemental Figure 1). This decreases the influence of erroneous high precision in some measurements, enabling the effect size to be determined by using a moving average of variability, which better approximates the variability at a given point. An effect size of 1.7 indicates that the mean of one group is positioned at the 95th percentile of the other group in a binary comparison 50. The use of Cohen’s d along with ANOVA calculations therefore enables a high degree of confidence that low P-values indeed demonstrate significance even for comparisons with lower apparent fold changes.