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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

From: Single-cell transcriptomics of popliteal lymphatic vessels and peripheral veins reveals altered lymphatic muscle and immune cell populations in the TNF-Tg arthritis model

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 1.21E87 & 3.99E87
Galnt15 Polypeptide N-acetylgalactosaminyl-transferase 15 1.26 & 1.28 5.5E117 & 4.11E62
Ccdc80 Coiled-coil Domain-Containing Protein 80 1.25 & 1.69 3.8E101 & 1.95E82
Zbtb16 Zinc Finger and BTB Domain-Containing Protein 16 1.17 & 1.07 2.9E139 & 1.84E75
Klf9 Krueppel-like Factor 9 1.10 & 1.08 2.8E122 & 1.62E57