6 Differential Expression Analysis II
Combined analysis with batch as a covariate
6.1 Handling Batch-Treatment Confounding
When treatment is nested within batch, any observed difference between Cre-AAV and GFP could potentially be attributed to either true biological effects of the treatment or technical batch effects. However, unlike complete confounding, our design does allow for batch adjustment because GFP control samples exist in both batches.
A model with ~ batch + Sex + group is mathematically valid: the batch effect can be estimated from GFP samples present in both batches, and the treatment effect is then estimated as the Cre-AAV versus GFP difference within Batch 2 after accounting for the batch effect.
6.2 Pre-filtering low count genes
Genes with very low read counts were excluded to minimize technical noise. After filtering for a minimum of 20 counts in at least five samples, approximately 19011 genes were retained for downstream analysis.
6.3 Differential expression analysis between Cre-AAV and GFP control groups in switch mice
Differential expression analysis was performed using DESeq2 with a design formula that explicitly modeled batch effects: ~ batch + Sex + group. GFP Control was set as the reference level for treatment comparison.
Our design involves the same mice measured across batches (paired structure) nested within a batch-treatment confound. The ideal model would be a mixed-effects model with random effects: Treatment + (1|MouseID) + (1|Batch) DESeq2’s standard framework assumes all samples are independent and cannot model the correlation between repeated measurements of the same biological individual through random effects (e.g., mouse-specific baseline expression). Retaining both measurements would violate this independence assumption. While removing Batch 1 duplicates would resolve this, we chose to collapse cross-batch measurements by averaging to preserve all sequencing data. This approach treats each mouse as a single biological unit, though it reduces variance by averaging over real batch-to-batch measurement variability. While this reduces variance by averaging over real batch-to-batch variability (potentially anti-conservative), PCA showed minimal batch effects.
Significance thresholds were set at FDR < 0.05 and |log₂FC| > 1, with subsequent filtering to remove pseudogenes, unannotated loci, mitochondrial genes, and ribosomal protein genes.
6.3.1 Liver
In liver tissue from all mice (males and females combined), we identified 121 significantly differentially expressed genes between Cre-AAV and GFP control animals (FDR < 0.05, |log2FC| > 1).
Diagnostic plots for the DE analysis
Diagnostic plots confirmed the validity of the analysis. The p-value distribution showed substantial enrichment for low p-values, indicating genuine differential expression rather than an all-noise result.
Most significant genes exhibited moderate to high expression levels (log₁₀ baseMean between 5 and 7), confirming that differential expression was primarily detected in well-expressed transcripts with sufficient statistical power. Very lowly expressed genes contributed minimally, further supporting the robustness of the filtering and normalization procedures.
Significantly differentially expressed genes in liver
Cre-AAV and GFP control
(FDR < 0.05, |log2FC| > 1)
| gene | baseMean | log2FoldChange | padj |
|---|---|---|---|
| Rps26-ps1 | 18.84 | -6.60 | 0.00 |
| Vcp-rs | 65.58 | -2.35 | 0.00 |
| Rpl18-ps2 | 30.06 | -2.97 | 0.00 |
| Gm8566 | 108.75 | -2.14 | 0.00 |
| Gm10073 | 33.39 | -2.97 | 0.00 |
| Gm10263 | 18.29 | -4.10 | 0.00 |
| Rpl28-ps1 | 58.47 | -1.93 | 0.00 |
| Gstm2-ps1 | 53.61 | -2.97 | 0.00 |
| Gm45855 | 32.41 | -2.00 | 0.00 |
| Gm4332 | 37.02 | -2.56 | 0.00 |
| Gm11478 | 50.89 | -2.14 | 0.00 |
| Glo1-ps | 43.49 | -2.06 | 0.00 |
| Gm16437 | 14.46 | -3.16 | 0.00 |
| Gm13611 | 13.15 | -4.32 | 0.00 |
| Gm15163 | 39.33 | -1.89 | 0.00 |
| ENSMUSG00000143433 | 29.55 | -2.66 | 0.00 |
| Gm9816 | 17.24 | -2.16 | 0.00 |
| Gm13436 | 32.37 | -2.70 | 0.00 |
| Gm10221 | 38.13 | -2.11 | 0.00 |
| Gm4366 | 59.20 | -1.37 | 0.00 |
| Glns-ps1 | 29.01 | -2.54 | 0.00 |
| Ccdc148 | 79.22 | 1.29 | 0.00 |
| Eef2-ps2 | 25.88 | -2.81 | 0.00 |
| mt-Ts1 | 8.98 | -4.92 | 0.00 |
| Gm12481 | 52.96 | -6.89 | 0.00 |
| Lrp1 | 8579.16 | -1.08 | 0.00 |
| Gm11964 | 10.61 | -3.07 | 0.00 |
| Cox5b-ps | 37.20 | -1.81 | 0.00 |
| Ftl1-ps1 | 524.56 | -1.42 | 0.00 |
| Gm14586 | 43.58 | -2.27 | 0.00 |
| 2810001A02Rik | 224.90 | 1.23 | 0.00 |
| Gm6180 | 6.73 | -3.00 | 0.00 |
| Gstp-ps | 133.94 | -2.17 | 0.00 |
| Slc41a2 | 264.20 | -1.91 | 0.00 |
| Rgs4 | 54.71 | 1.19 | 0.00 |
| Eno1b | 38.52 | -2.73 | 0.00 |
| Mmp7 | 15.72 | 4.03 | 0.00 |
| Gm8730 | 51.91 | -2.43 | 0.00 |
| Rpl7-ps7 | 12.77 | -1.98 | 0.00 |
| Rps18-ps5 | 46.29 | -2.48 | 0.00 |
| Gm9794 | 75.37 | -1.43 | 0.00 |
| Gm7600 | 16.38 | -2.82 | 0.00 |
| Gm7049 | 17.59 | -2.20 | 0.00 |
| Bnip3 | 12935.81 | 1.05 | 0.00 |
| Gm6204 | 32.82 | -2.68 | 0.00 |
| Gm5805 | 13.88 | -3.10 | 0.00 |
| Mov10 | 216.39 | -1.22 | 0.00 |
| Arg2 | 13.53 | 2.31 | 0.00 |
| Mif-ps4 | 9.50 | -3.53 | 0.00 |
| ENSMUSG00000140143 | 99.65 | 2.25 | 0.00 |
| ENSMUSG00000121793 | 109.23 | -1.72 | 0.00 |
| ENSMUSG00000128633 | 94.62 | -2.10 | 0.00 |
| Gm10076 | 1830.86 | 1.10 | 0.00 |
| Gm10874 | 21.94 | -1.72 | 0.00 |
| ENSMUSG00000139771 | 170.64 | -1.66 | 0.00 |
| Lncbate1 | 94.08 | 1.37 | 0.00 |
| Gm5540 | 32.59 | -2.30 | 0.00 |
| Gm5456 | 15.84 | -2.87 | 0.00 |
| Gm4149 | 35.41 | -2.08 | 0.00 |
| Gm12350 | 33.93 | -1.94 | 0.00 |
| Gm12174 | 27.14 | -2.06 | 0.00 |
| Gm10232 | 15.91 | -2.22 | 0.00 |
| E030018B13Rik | 64.34 | 4.89 | 0.00 |
| Gm16573 | 624.05 | 1.50 | 0.00 |
| Rps10-ps1 | 15.50 | -3.15 | 0.00 |
| Gm9755 | 21.25 | -1.95 | 0.00 |
| Gm2962 | 11.66 | -2.48 | 0.00 |
| Slc36a1 | 409.28 | -1.03 | 0.00 |
| Gm44170 | 66.88 | -1.72 | 0.00 |
| ENSMUSG00000135866 | 247.05 | -2.93 | 0.00 |
| Snhg3 | 225.84 | 1.56 | 0.00 |
| Myorg | 671.66 | -1.07 | 0.00 |
| Abca2 | 552.28 | -1.25 | 0.00 |
| Rab11b-ps2 | 4.83 | -3.51 | 0.00 |
| Gm10039 | 20.42 | -1.90 | 0.00 |
| Nhsl3 | 894.50 | -1.10 | 0.00 |
| Mrpl23-ps1 | 12.15 | -2.06 | 0.00 |
| Gm56915 | 65.26 | 1.33 | 0.00 |
| Gm6652 | 275.97 | -1.11 | 0.00 |
| Cd83 | 93.84 | 1.45 | 0.00 |
| C4b | 16639.92 | -1.04 | 0.00 |
| ENSMUSG00000126438 | 14.80 | -2.41 | 0.00 |
| Gm6733 | 15.30 | -2.05 | 0.00 |
| Rpl17-ps3 | 57.80 | -1.67 | 0.00 |
| Mmp15 | 527.71 | -1.23 | 0.00 |
| Pgam1-ps2 | 24.37 | -1.83 | 0.00 |
| ENSMUSG00000121505 | 150.78 | 1.60 | 0.00 |
| Gm10288 | 116.74 | -1.48 | 0.00 |
| Adrm1b | 37.12 | -1.71 | 0.01 |
| Ptprf | 2408.30 | -1.08 | 0.01 |
| Gm57111 | 135.57 | 1.68 | 0.01 |
| Gm12918 | 87.62 | -1.41 | 0.01 |
| Rpl19-ps11 | 113.24 | -1.12 | 0.01 |
| Got2-ps1 | 61.42 | -1.01 | 0.01 |
| Gm4459 | 14.98 | -2.13 | 0.01 |
| ENSMUSG00000137723 | 178.93 | 1.39 | 0.01 |
| Rps16-ps2 | 81.63 | -1.49 | 0.01 |
| Hspd1-ps3 | 59.73 | -1.01 | 0.01 |
| Gm12251 | 16.03 | -1.87 | 0.01 |
| ENSMUSG00000142392 | 13.48 | 6.79 | 0.01 |
| Znf41-ps | 5.56 | 17.34 | 0.01 |
| Abca3 | 1162.54 | -1.05 | 0.01 |
| Gm5422 | 13.91 | -2.38 | 0.01 |
| Sntg1 | 9.52 | 2.94 | 0.01 |
| Tpt1-ps3 | 147.96 | -1.14 | 0.01 |
| Gpi-ps | 16.78 | -2.09 | 0.01 |
| Gm9616 | 14.66 | -2.26 | 0.01 |
| Rps3a2 | 79.40 | -1.17 | 0.01 |
| Rpl23a-ps3 | 34.34 | -1.59 | 0.01 |
| Col1a1 | 50.22 | -1.25 | 0.01 |
| Gm10819 | 7.05 | -2.83 | 0.01 |
| Gm9625 | 29.65 | -1.56 | 0.01 |
| Gm12751 | 42.57 | 1.40 | 0.01 |
| Sap18b | 38.87 | -1.28 | 0.01 |
| Rps15-ps2 | 8.18 | -2.50 | 0.01 |
| Gm28857 | 68.21 | 2.11 | 0.01 |
| Hspe1-rs1 | 39.18 | -1.58 | 0.01 |
| Rpl35rt | 122.60 | -1.57 | 0.01 |
| Mfhas1 | 318.41 | -1.03 | 0.01 |
| Fn1 | 19990.89 | -1.11 | 0.01 |
| E230001N04Rik | 24.89 | 2.48 | 0.01 |
To focus on high-confidence, biologically interpretable results, we applied an additional filtering step to remove pseudogenes (-ps, -rs), unannotated loci (Gm-, Rik, ENSMUS), mitochondrial (-mt), and ribosomal (-Rp) genes. This yielded 26 high-confidence nuclear genes that were consistently dysregulated in response to Cre-mediated ApoE4→ApoE2 conversion in liver, after adjusting for both sex and batch effects.
| gene | baseMean | log2FoldChange | padj |
|---|---|---|---|
| Ccdc148 | 79.22 | 1.29 | 0.00 |
| Lrp1 | 8579.16 | -1.08 | 0.00 |
| Slc41a2 | 264.20 | -1.91 | 0.00 |
| Rgs4 | 54.71 | 1.19 | 0.00 |
| Eno1b | 38.52 | -2.73 | 0.00 |
| Mmp7 | 15.72 | 4.03 | 0.00 |
| Bnip3 | 12935.81 | 1.05 | 0.00 |
| Mov10 | 216.39 | -1.22 | 0.00 |
| Arg2 | 13.53 | 2.31 | 0.00 |
| Lncbate1 | 94.08 | 1.37 | 0.00 |
| Slc36a1 | 409.28 | -1.03 | 0.00 |
| Snhg3 | 225.84 | 1.56 | 0.00 |
| Myorg | 671.66 | -1.07 | 0.00 |
| Abca2 | 552.28 | -1.25 | 0.00 |
| Nhsl3 | 894.50 | -1.10 | 0.00 |
| Cd83 | 93.84 | 1.45 | 0.00 |
| C4b | 16639.92 | -1.04 | 0.00 |
| Mmp15 | 527.71 | -1.23 | 0.00 |
| Adrm1b | 37.12 | -1.71 | 0.01 |
| Ptprf | 2408.30 | -1.08 | 0.01 |
| Abca3 | 1162.54 | -1.05 | 0.01 |
| Sntg1 | 9.52 | 2.94 | 0.01 |
| Col1a1 | 50.22 | -1.25 | 0.01 |
| Sap18b | 38.87 | -1.28 | 0.01 |
| Mfhas1 | 318.41 | -1.03 | 0.01 |
| Fn1 | 19990.89 | -1.11 | 0.01 |
6.3.2 Brain
In brain tissue from all mice, we identified 150 significantly differentially expressed genes between Cre-AAV and GFP control animals using the same statistical approach and thresholds (FDR < 0.05, |log2FC| > 1).
Diagnostic plots for the DE analysis
Diagnostic plots revealed that the p-value distribution from the Wald test was approximately uniform with no substantial enrichment of low p-values, suggesting a more modest transcriptional response in brain compared to liver. Nevertheless, the log₁₀ baseMean distribution for significant genes displayed moderate to high expression levels, indicating that detected changes occurred in well-expressed genes.
Significantly differentially expressed genes in brain
Cre-AAV and GFP control
(FDR < 0.05, |log2FC| > 1)
| gene | baseMean | log2FoldChange | padj |
|---|---|---|---|
| Gm15427 | 62.49 | -2.26 | 0.00 |
| Rpl35rt | 127.75 | -2.50 | 0.00 |
| Rpsa-ps10 | 72.78 | -2.05 | 0.00 |
| Cox5b-ps | 35.24 | -2.07 | 0.00 |
| Gm10288 | 97.74 | -1.96 | 0.00 |
| Rps16-ps2 | 55.97 | -2.35 | 0.00 |
| Rps6-ps4 | 115.70 | -1.24 | 0.00 |
| Rps19-ps6 | 38.23 | -2.75 | 0.00 |
| Gm4149 | 31.98 | -2.53 | 0.00 |
| Rps26-ps1 | 14.16 | -5.64 | 0.00 |
| Rps3a2 | 68.28 | -1.92 | 0.00 |
| 4632415L05Rik | 14.57 | -5.24 | 0.00 |
| Rpl19-ps11 | 99.78 | -1.79 | 0.00 |
| Gm10073 | 41.80 | -2.71 | 0.00 |
| Rpl17-ps10 | 78.73 | -1.81 | 0.00 |
| Gm6560 | 72.20 | -1.37 | 0.00 |
| ENSMUSG00000136525 | 49795.59 | 0.84 | 0.00 |
| Gm11478 | 43.76 | -2.41 | 0.00 |
| Rps18-ps5 | 21.26 | -3.69 | 0.00 |
| Rpl14-ps1 | 56.17 | -1.53 | 0.00 |
| Rpl17-ps3 | 50.93 | -2.15 | 0.00 |
| ENSMUSG00000121793 | 81.80 | -2.33 | 0.00 |
| Eno1b | 46.81 | -2.12 | 0.00 |
| Gm13456 | 187.81 | -1.36 | 0.00 |
| Rpl3-ps1 | 182.80 | -1.08 | 0.00 |
| Rps18-ps6 | 37.32 | -2.34 | 0.00 |
| Rpl23a-ps3 | 35.90 | -1.85 | 0.00 |
| Gm4332 | 27.77 | -2.94 | 0.00 |
| Rps13-ps1 | 30.42 | -2.42 | 0.00 |
| Gm9385 | 45.24 | -1.82 | 0.00 |
| ENSMUSG00000121779 | 68.48 | -1.07 | 0.00 |
| Gm13436 | 23.64 | -3.16 | 0.00 |
| Uba52rt | 148.07 | -1.35 | 0.00 |
| Gm13611 | 9.55 | -4.67 | 0.00 |
| ENSMUSG00000143433 | 23.47 | -2.86 | 0.00 |
| Gm9794 | 52.50 | -1.63 | 0.00 |
| Gm14586 | 31.13 | -2.25 | 0.00 |
| ENSMUSG00000132604 | 24.15 | -2.24 | 0.00 |
| Rps23-ps1 | 47.48 | -1.86 | 0.00 |
| Rps25-ps1 | 12.78 | -3.35 | 0.00 |
| Gm7600 | 16.89 | -2.87 | 0.00 |
| Rpl9-ps6 | 211.35 | -1.41 | 0.00 |
| Gm11223 | 38.17 | -1.56 | 0.00 |
| Gm8730 | 21.73 | -2.83 | 0.00 |
| Gm8203 | 15.74 | -2.36 | 0.00 |
| Rps15a-ps7 | 15.33 | -2.27 | 0.00 |
| Gm7308 | 39.44 | -1.47 | 0.00 |
| Gm7536 | 94.83 | -1.53 | 0.00 |
| ENSMUSG00000121784 | 146.55 | -1.04 | 0.00 |
| Oaz1-ps | 63.97 | -1.58 | 0.00 |
| Gm8566 | 20.17 | -2.14 | 0.00 |
| Gm9493 | 31.73 | -1.93 | 0.00 |
| Rplp2-ps1 | 22.23 | -3.29 | 0.00 |
| Gm4366 | 82.42 | -1.31 | 0.00 |
| Gm6204 | 28.49 | -2.70 | 0.00 |
| Gm15772 | 27.58 | -2.14 | 0.00 |
| Gm5436 | 14.19 | -2.57 | 0.00 |
| Gm5805 | 12.05 | -3.52 | 0.00 |
| Gm37530 | 12.73 | 2.30 | 0.00 |
| Fus | 4486.34 | 0.34 | 0.00 |
| Gm12892 | 88.89 | -1.29 | 0.00 |
| Rps27a-ps2 | 48.15 | -1.41 | 0.00 |
| Gm4202 | 64.89 | -1.10 | 0.00 |
| Ndufs7 | 1547.25 | -0.45 | 0.00 |
| Ndufa5 | 1405.95 | -0.36 | 0.00 |
| Gm10263 | 12.36 | -3.43 | 0.00 |
| Gan | 640.17 | 0.32 | 0.00 |
| Ftl1-ps1 | 45.47 | -1.53 | 0.00 |
| Gm6710 | 221.28 | -0.65 | 0.00 |
| ENSMUSG00000140457 | 486.34 | 0.78 | 0.00 |
| Gm8355 | 59.14 | -1.07 | 0.00 |
| Rps7-ps3 | 49.67 | -1.95 | 0.00 |
| Rpl18-ps2 | 19.31 | -2.75 | 0.00 |
| Gm5499 | 26.90 | -1.55 | 0.00 |
| Gm6789 | 41.50 | -1.14 | 0.00 |
| Rpl36a-ps2 | 20.10 | -1.81 | 0.00 |
| Aldoart1 | 15.29 | -2.54 | 0.00 |
| Rpl35a-ps3 | 34.77 | 20.50 | 0.00 |
| ENSMUSG00000139771 | 140.98 | -1.92 | 0.00 |
| Rpl10a-ps1 | 65.56 | -1.00 | 0.00 |
| Rps10-ps2 | 42.98 | -1.33 | 0.00 |
| Gm8226 | 79.61 | -1.11 | 0.00 |
| Pgam1-ps2 | 69.70 | -1.62 | 0.00 |
| Ap2m1-ps | 153.16 | -0.79 | 0.00 |
| Gstp-ps | 13.32 | -2.30 | 0.00 |
| Dock9 | 3143.58 | 0.27 | 0.00 |
| Rpl37rt | 29.46 | -5.75 | 0.00 |
| Endog | 301.92 | -0.52 | 0.00 |
| Nrtn | 72.99 | -0.92 | 0.00 |
| 1810049J17Rik | 13.61 | -3.05 | 0.00 |
| Zmat5 | 271.78 | -0.43 | 0.00 |
| Rpl28-ps1 | 39.16 | -1.84 | 0.00 |
| Dido1 | 1334.11 | 0.26 | 0.00 |
| Gm16437 | 13.68 | -2.18 | 0.00 |
| Gm6863 | 45.91 | -1.32 | 0.00 |
| Rps24-ps3 | 27.59 | -2.13 | 0.00 |
| Fkbp1b | 449.39 | -0.29 | 0.00 |
| Olig1 | 2326.62 | -0.35 | 0.00 |
| Tnrc6c | 1786.75 | 0.37 | 0.00 |
| Gm6180 | 27.34 | -1.48 | 0.00 |
| Gm12174 | 18.35 | -2.03 | 0.00 |
| Ube2n-ps1 | 15.64 | -1.65 | 0.00 |
| Mif-ps4 | 10.48 | -3.36 | 0.00 |
| Gm14121 | 10.89 | -2.17 | 0.00 |
| ENSMUSG00000121655 | 13.32 | -1.95 | 0.00 |
| Pcsk1n | 9849.26 | -0.53 | 0.00 |
| Gm6170 | 4.66 | -3.46 | 0.00 |
| Tmem223 | 586.05 | -0.42 | 0.00 |
| ENSMUSG00000121777 | 299.91 | -0.97 | 0.00 |
| Kmt2d | 1891.12 | 0.41 | 0.00 |
| 4933431K14Rik | 67.96 | -0.80 | 0.00 |
| Srrm4 | 875.61 | 0.33 | 0.00 |
| Gm12254 | 19.49 | -1.69 | 0.00 |
| Bicral | 1162.75 | 0.25 | 0.00 |
| Gm10052 | 37.93 | -0.98 | 0.00 |
| Gpi-ps | 58.96 | -1.27 | 0.00 |
| Rps10-ps1 | 13.08 | -2.74 | 0.00 |
| ENSMUSG00000121783 | 447.07 | -0.85 | 0.00 |
| Kmt2a | 2860.62 | 0.33 | 0.00 |
| Gria2 | 10476.71 | 0.27 | 0.00 |
| Gm9816 | 29.45 | -1.56 | 0.00 |
| Pigyl | 436.88 | -0.44 | 0.00 |
| Gm3571 | 7.47 | -3.33 | 0.01 |
| Rbm25 | 2275.66 | 0.36 | 0.01 |
| Lars2 | 32337.98 | 0.83 | 0.01 |
| Cdr1 | 119.55 | 1.24 | 0.01 |
| Dohh | 1074.71 | -0.41 | 0.01 |
| ENSMUSG00000128633 | 85.79 | -2.98 | 0.01 |
| Gm10250 | 42.45 | -1.38 | 0.01 |
| Gm10221 | 21.83 | -1.99 | 0.01 |
| Wdr89 | 111.21 | -0.66 | 0.01 |
| Rpl31-ps8 | 53.56 | -1.35 | 0.01 |
| Nudc-ps1 | 12.73 | -1.88 | 0.01 |
| Ramp1 | 1295.27 | -0.36 | 0.01 |
| Sap18b | 30.52 | -1.37 | 0.01 |
| Gm4459 | 11.16 | -2.27 | 0.01 |
| Hspe1-rs1 | 14.02 | -2.19 | 0.01 |
| Atp6v0c-ps2 | 39.64 | -1.13 | 0.01 |
| ENSMUSG00000137224 | 84.10 | -1.16 | 0.01 |
| Gfra4 | 735.38 | -0.30 | 0.01 |
| Stmn3 | 10342.08 | -0.32 | 0.01 |
| Mt3 | 4865.41 | -0.38 | 0.01 |
| Nopchap1 | 1134.99 | 0.31 | 0.01 |
| P3h4 | 305.18 | -0.42 | 0.01 |
| Rftn2 | 724.62 | -0.28 | 0.01 |
| B020010K11Rik | 32.09 | -2.03 | 0.01 |
| Tnrc6b | 2113.46 | 0.36 | 0.01 |
| Mrpl12 | 1167.93 | -0.42 | 0.01 |
| 375.24 | -0.41 | 0.01 | |
| Fbxl15 | 321.95 | -0.53 | 0.01 |
After applying the same filtering criteria to exclude pseudogenes, unannotated loci, mitochondrial genes, and ribosomal protein genes, we retained 5 high-confidence nuclear genes that showed consistent dysregulation in brain tissue following Cre-mediated ApoE4→ApoE2 conversion, adjusted for batch and sex.
| gene | baseMean | log2FoldChange | padj |
|---|---|---|---|
| Eno1b | 46.81 | -2.12 | 0.00 |
| Uba52rt | 148.07 | -1.35 | 0.00 |
| Aldoart1 | 15.29 | -2.54 | 0.00 |
| Cdr1 | 119.55 | 1.24 | 0.01 |
| Sap18b | 30.52 | -1.37 | 0.01 |
6.3.3 Common DEGs in liver and brain
To identify core molecular responses to ApoE isoform conversion that occur independently of tissue context, we intersected the lists of high-confidence DEGs from liver and brain. In the batch-adjusted analysis, only 2 genes were significantly differentially expressed in both tissues:
Eno1b, Sap18b