Table 2 Differentially regulated genes in TNF-Tg vs WT mice common between LMCs and VSMCs. Mt2 (and Mt1, omitted for redundancy), Timp1, Mmp3, Prg4, and Cxcl12 are the top 5 upregulated genes in tumor necrosis factor transgenic (TNF-Tg) lymphatic muscle cells (LMCs) that similarly demonstrate increased expression in TNF-Tg vascular smooth muscle cells (VSMCs) (bold). On the other hand, Apod, Galnt15, Ccdc80, Zbtb16, and Klf9 are the top 5 downregulated genes in TNF-Tg LMCs that were also differentially expressed in TNF-Tg VSMCs (not bold). Proteins coded by the gene, log2 fold-change (log2FC), and false discovery rates (FDRs) for LMCs and VSMCs are provided. The top 5 genes were ranked based on log2FC effect size with an FDR < 0.01. The genes were selected by evaluating the top up- or downregulated genes for LMCs and listed if the particular genes were also differentially regulated in VSMCs. The LMC and VSMC populations were defined based on the wild-type (WT) and TNF-Tg integrated datasets in Fig. 3. A complete list of differentially expressed genes in TNF-Tg mice for both LMC and VSMC populations is provided in the Supplementary Materials
Gene | Protein | Avg Log2FC (LMC & VSMC) | FDR (LMC & VSMC) |
|---|---|---|---|
Mt2 | Metallothionein 2 | 2.08 & 1.19 | 2.26E−20 & 1.04E−13 |
Timp1 | Timp1 | 1.69 & 1.61 | 7.79E−91 & 1.59E−65 |
Mmp3 | Matrix Metalloproteinase-3 | 1.65 & 1.41 | 5.58E−40 & 1.27E−61 |
Prg4 | Proteoglycan 4 / Lubrican | 1.56 & 1.46 | 7.71E−34 & 1.08E−43 |
Cxcl12 | C-X-C Motif Chemokine 12 | 1.54 & 0.69 | 2.59E−76 & 4.77E−21 |
Apod | Apolipoprotein D | − 1.30 & − 1.61 | 1.21E−87 & 3.99E−87 |
Galnt15 | Polypeptide N-acetylgalactosaminyl-transferase 15 | − 1.26 & − 1.28 | 5.5E−117 & 4.11E−62 |
Ccdc80 | Coiled-coil Domain-Containing Protein 80 | − 1.25 & − 1.69 | 3.8E−101 & 1.95E−82 |
Zbtb16 | Zinc Finger and BTB Domain-Containing Protein 16 | − 1.17 & − 1.07 | 2.9E−139 & 1.84E−75 |
Klf9 | Krueppel-like Factor 9 | − 1.10 & − 1.08 | 2.8E−122 & 1.62E−57 |