Table 2.
Summary of additional genes tested by qPCR. The list includes differentially expressed (DE) genes overlapping between cerebellum and blood, some genes selected for their high fold change in blood and some genes selected from predicted dysregulated pathways. Log2FC refers to the ratio Mecp2-null/WT; hence, positive values mean upregulation in Mecp2-null and vice versa.
| Additional genes tested by qPCR | ||||
|---|---|---|---|---|
| Genes identified in cerebellum that are also significant in blood | ||||
| Gene | log2FC cerebellum | FDR cerebellum | log2FC blood | Uncorrected p-value blood |
| Dnah14 | 2.04 | 2.51E-02 | 8.54 | 3.88E-03 |
| Fkbp5 | 1.33 | 3.70E-02 | 1.40 | 4.90E-03 |
| Serpina1c | −10.52 | 2.76E-02 | 9.87 | 5.50E-03 |
| Gm28374 | 6.52 | 1.34E-02 | −6.55 | 1.84E-02 |
| Lsm12 | 1.91 | 5.39E-19 | −1.30 | 3.24E-02 |
| Paip2 | 1.00 | 1.06E-04 | −1.06 | 3.49E-02 |
| Ahsa2 | −0.85 | 4.13E-02 | −0.83 | 4.15E-02 |
| Mup10 | −10.75 | 3.30E-02 | 7.12 | 4.28E-02 |
| Genes identified in blood that are also significant in cerebellum | ||||
| Gene | log2FC blood | FDR blood | log2FC cerebellum | Uncorrected p-value cerebellum |
| Atp6v0d2 | 10.74 | 4.30E-02 | 5.91 | 3.44E-04 |
| Hal | 9.73 | 2.87E-02 | −5.88 | 3.65E-04 |
| Ankrd63 | 8.90 | 3.79E-02 | 2.07 | 5.56E-04 |
| Hist1h2be | −3.32 | 1.08E-02 | −0.86 | 4.59E-03 |
| Slc6a4 | −1.99 | 2.27E-02 | 2.75 | 1.13E-02 |
| Crispld2 | 2.54 | 4.87E-02 | 0.66 | 1.22E-02 |
| RP23-253I14.4 | 11.74 | 1.05E-02 | 3.12 | 1.28E-02 |
| C430002N11Rik | −8.55 | 5.89E-03 | 4.84 | 1.32E-02 |
| Tnnc2 | 10.97 | 6.73E-09 | 3.44 | 1.37E-02 |
| Scgb3a2 | 14.25 | 2.26E-03 | 4.57 | 1.91E-02 |
| Mpo | 10.18 | 1.75E-06 | 1.18 | 2.65E-02 |
| Gm5741 | −8.52 | 9.00E-03 | 2.67 | 3.33E-02 |
| Gpx3 | 3.03 | 1.64E-02 | 0.73 | 3.37E-02 |
| High fold change in blood | ||||
| Gene | log2FC RNAseq | FDR RNAseq | ||
| S100a9 | 2.87 | 2.01E-02 | ||
| Snx31 | −8.80 | 3.09E-03 | ||
| Ms4a3 | 13.05 | 5.27E-03 | ||
| Prg3 | 12.26 | 5.27E-03 | ||
| Genes from predicted dysregulated pathways (blood) | ||||
| Gene | log2FC RNAseq | FDR RNAseq | ||
| Gsta3 | 8.98 | 4.06E-03 | ||
| Gstm2 | 7.56 | 2.34E-04 | ||
| Itgb3 | −3.15 | 1.00E-03 | ||