Table II.
List of differentially expressed genes between PCV2-inoculated and control pigs in mediastinal lymph node samples with the Affymetrix Porcine Genechip.
| Probe ID | Gene symbol | Gene name | Log2 FC | FDR | Biological processes |
|---|---|---|---|---|---|
| Globally down-regulated genes | |||||
| Ssc.17815.1.S1_at | LGALS3 | Lectin, galactoside-binding, soluble, 3 | −1.50 | 0.009 | Extracellular matrix organization |
| Ssc.575.1.S1_at | ACP5 | Acid phosphatase 5, tartrate resistant | −1.24 | 0.009 | Response to stimulus |
| Ssc.22441.1.A1_at | – | Annotation not clear | −1.20 | 0.024 | |
| Ssc.300.1.S1_at | SLC11A1 | Solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1 | −1.08 | 0.097 | Immune response |
| Ssc.20870.1.S1_at | FBLN1 | Fibulin-1 | −1.07 | 0.007 | Cell adhesion |
| Ssc.7212.1.A1_at | TFPI | Tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) | −1.07 | 0.051 | Blood coagulation |
| Ssc.115.1.S1_s_at | HMOX1 | Heme oxygenase (decycling) 1 | −1.05 | 0.028 | Apoptosis, cytokine production, catabolic process |
| Ssc.13115.1.A1_at | CXADR | Coxsackie virus and adenovirus receptor | −1.01 | 0.008 | Cell adhesion |
| Early up-regulated genes | |||||
| Ssc.19089.1.A1_at | Annotation not clear | 1.00 | 0.037 | ||
| Ssc.10588.1.A1_at | H28 | Histocompatibility 28 | 1.01 | 0.048 | Immune response |
| Ssc.30724.1.S1_at | HERC6 | Hect domain and RLD 6 | 1.03 | 0.069 | Ubiquitin-cycle |
| Ssc.29054.3.S1_at | GBP1 | Guanylate binding protein 1 | 1.03 | 0.044 | Immune response |
| Ssc.7116.1.A1_at | NT5C3 | 5′-nucleotidase, cytosolic III | 1.05 | 0.045 | Metabolic process |
| Ssc.26189.1.S1_a_at | RTP4 | Receptor (chemosensory) transporter protein 4 | 1.07 | 0.097 | Response to stimulus |
| Ssc.2641.1.S1_at | UBE2L6 | Ubiquitin-conjugating enzyme E2L 6 | 1.08 | 0.045 | Ubiquitin cycle |
| Ssc.883.1.S1_a_at | GBP2 | Guanylate binding protein 2 | 1.12 | 0.051 | Immune response |
| Ssc.336.1.S1_at | USP18 | Ubiquitin specific peptidase 18 | 1.13 | 0.083 | Ubiquitin cycle |
| Ssc.6433.2.S1_at | – | Annotation not clear | 1.13 | 0.084 | |
| Ssc.26009.1.S1_at | – | Annotation not clear | 1.16 | 0.082 | |
| Ssc.10593.1.S1_at | H28 | Histocompatibility 28 | 1.17 | 0.051 | Immune response |
| Ssc.9327.1.A1_at | HSH2D | Hematopoietic SH2 domain containing | 1.18 | 0.031 | Leukocyte activation |
| Ssc.7558.1.A1_at | – | Annotation not clear | 1.20 | 0.033 | |
| Ssc.29054.2.S1_at | GBP1 | Guanylate binding protein 1 | 1.30 | 0.033 | Immune response |
| Ssc.221.1.S1_at | MX1 | Myxovirus (influenza virus) resistance 1 | 1.41 | 0.070 | Response to virus, apoptosis |
| Ssc.17894.1.A1_at | – | Annotation not clear | 1.47 | 0.042 | |
| Ssc.5020.1.S1_at | SERPINA3 | Serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 | 1.50 | 0.057 | Response to stimulus |
| Ssc.11557.1.A1_at | ISG15 | ISG15 ubiquitin-like modifier | 1.78 | 0.090 | Ubiquitin cycle |
| Ssc.1031.1.S1_at | OAS1 | 2′-5′-oligoadenylate synthetase 1 | 1.82 | 0.089 | Immune response |
| SscAffx.1.1.S1_at | ISG20 | Interferon stimulated exonuclease gene 20 kDa | 1.88 | 0.031 | Response to virus |
| Ssc.286.1.S1_s_at | RSAD2 | Radical S-adenosyl methionine domain containing 3 | 2.16 | 0.052 | Response to virus |
| AFFX-Ss_IRP_3_at | RSAD2 | Radical S-adenosyl methionine domain containing 2 | 2.29 | 0.064 | Response to virus |
| Late up-regulated genes | |||||
| Ssc.23658.1.S1_at | PACAP | Proapoptotic caspase adaptor protein | 1.00 | 0.019 | Apoptosis |
| Ssc.21217.1.A1_at | GCUD2 | Gastric cancer up-regulated-2 | 1.01 | 0.019 | Unknown |
| Ssc.24982.1.S1_at | FABP7 | Fatty acid-binding protein 7, brain | 1.03 | 0.041 | Cell proliferation |
| Ssc.19400.2.A1_at | - | Annotation not clear | 1.03 | 0.041 | |
| Ssc.11070.1.S1_at | IgG | Immunoglobulin G | 1.13 | 0.098 | Immune response |
| Ssc.10498.1.A1_at | EAF2 | ELL associated factor 2 | 1.14 | 0.019 | Apoptosis, regulation of transcription |
| Ssc.13778.1.S1_at | IgG | Immunoglobulin G | 1.15 | 0.024 | |
| Ssc.12505.1.A1_at | CLGN | Calmegin | 1.28 | 0.007 | Protein binding |
| Ssc.15942.2.S1_x_at | Ig VDJ | Ig heavy chain variable region (VDJ) | 1.38 | 0.046 | Immune response |
| Ssc.15942.3.S1_x_at | Ig VDJ | Ig heavy chain variable region (VDJ) | 1.47 | 0.051 | Immune response |
| Ssc.4093.1.A1_at | IFNG | Interferon gamma | 1.54 | 0.009 | Cytokine production, apoptosis |
| Ssc.23408.1.A1_s_at | – | Annotation not clear | 1.63 | 0.024 | |
LogFC: log fold change, FDR: false discovery rate.