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Table 1 Functional grouping of genes differentially expressed (≥2-fold and P < 0.05, n = 3) between PCV2-infected and mock-infected control

From: Transcription analysis of the porcine alveolar macrophage response to porcine circovirus type 2

Functional classification Gene name Gene symbol 24 HPI FC Q-value, % (24hpi) 48 HPI FC Q-value, % (48hpi) GenBank ID
Immune response
  rho GDP dissociation inhibitor beta ARHGDIB 2.16 0.41 1.21 13.11 NM_001009600
  CMRF35-like molecule 1 CLM1 2.35 0.95 1.38 13.11 AY457047
  cathepsin C CTSC 2.12 3.06 1.74 11.46 NM_001814
  cathepsin S CTSS 0.5 1.09 0.77 19.25 M90696.1
  Fc fragment of IgG low affinity II b receptor FCGR2B 3.47 0.54 1.85 8.49 NM_001033013
  neutrophil cytosolic factor 4 NCF4 2.62 0 2.12 6.28 NM_000631
Humoral immune response
  chemokine ligand 16 CCL16 3.85 4.64 3.24 4.93 NM_004590;
  CD74 molecule CD74 3.94 0 3.43 0.58 NM_213774
  complement factor D CFD 0.36 0.41 0.59 2.88 NM_001928
  C-type lectin domain family 2, member B CLEC2B 2.83 1.62 2.10 1.09 NM_005127
Inflammatory response
  chemokine ligand 3-like 3 CCL3L3 7.58 0 2.46 1.64 NM_001001437
  chemokine Ligand 5 CCL5 1.53 14.04 2.25 2.44 AK312212
  chemokine ligand 5 CXCL5 32.28 0 12.96 0 EU176356
  chemokine ligand 7 CXCL7 2.75 0.95 3.57 1.97 NM_213862.1
  interleukin-6 IL6 2.26 4.65 1.36 13.43 NM_214399.1
  S100 calcium binding protein A1 S100A1 0.31 0.41 0.40 0.71 NM_006271
  S100 calcium binding protein A12 S100A12 10.98 0 5.13 1.09 FJ263393.1
  S100 calcium binding protein A8 S100A8 12.96 0 6.83 0 FJ263391.1
  S100 calcium binding protein A9 S100A9 20.00 0 9.71 0 FJ263392.1
  serum amyloid A1 SAA1 14.59 0.54 1.82 24.35 NM_199161
  secreted phosphoprotein 1 SPP1 2.66 2.39 1.67 24.35 AK296035
  tumor necrosis factor, alpha-induced protein 6 TNFAIP6 6.54 0 3.26 0.58 NM_001159607
Lipid biosynthesis
  Lysophosphatidic acid acyltransferase, delta AGPAT4 2.34 0 1.48 0.58 NM_020133
  lysophosphatidic acid acyltransferase, zeta AGPAT6 1.56 0.54 2.03 0 NM_178819
  alkylglycerone phosphate synthase AGPS 2.41 0.95 1.46 32.28 NM_003659
  farnesyl-diphosphate farnesyltransferase 1 FDFT1 0.77 14.04 0.45 1.82 AK297868
  isopentenyl-diphosphate delta isomerase 1 IDI1 0.84 26.53 0.46 2.88 NM_004508
  inositol-3-phosphate synthase 1 ISYNA1 2.12 0.54 1.65 1.44 NM_016368
  stearoyl-CoA desaturase SCD 2.46 0.54 3.37 8.49 AB208982
  triosephosphate isomerase 1 TPI1 3.00 0 2.11 3.33 NM_000365
Locomotion
  CD97 molecule CD97 1.50 3.06 2.17 1.64 NM_001784
  coronin, actin binding protein, 1A CORO1A 2.64 0.54 1.26 4.65 NM_007074
  chemokine ligand 10 CXCL10 7.69 4.93 2.58 1.07 NM_001565
  Kallmann syndrome 1 sequence KAL1 0.43 1.44 0.46 4.65 NM_000216
  mitogen-activated protein kinase 1 MAP2K1 2.03 0 1.17 1.7 NM_002755
  platelet factor 4 PF4 4.15 0 3.80 1.64 NM_002619
  phosphatidic acid phosphatase type 2B PPAP2B 8.45 0.95 3.04 11.46 NM_003713
  prostaglandin-endoperoxide synthase 2 PTGS2 5.75 0 5.41 0 NM_001784
Lyase activity
  aldolase C, fructose-bisphosphate ALDOC 3.08 0 2.18 3.33 AK294157
  carbonic anhydrase XIII CA13 0.41 0.82 0.40 0.71 NM_198584
  enolase 1, (alpha) ENO1 2.24 0 1.80 4.94 AK298600
  N-acetylneuraminate pyruvate lyase NPL 1.71 1.62 2.28 0 AK297017
  serine dehydratase SDS 7.58 0 9.14 0 NM_006843
Antigen processing and presentation
  Major histocompatibility complex, class II, DO alpha DOA 2.29 0 1.42 13.11 NM_002119.3
  Major histocompatibility complex, class II, DO beta DOB 17.85 2.39 3.78 1.64 NM_002120.3
  Major histocompatibility complex, class II, DQ alpha 1 DQA1 2.07 1.62 1.37 9.21 M33906.1
  Major histocompatibility complex, class II, DQ beta 1 DQB1 2.47 0 2.14 11.46 M32577
  Major histocompatibility complex, class II, DR alpha DRA 7.87 0 3.69 1.08 NM_001134339
  Major histocompatibility complex, class II, DR beta 1 DRB1 5.83 0.95 2.17 1.17 AY770514.1
Signal transducer activity
  guanine nucleotide binding protein (G protein), gamma 2 GNG2 1.94 0.41 2.26 0.42 NM_0530
  regulator of G-protein signaling 1 RGS1 1.02 58.23 0.47 4.25 NM_002922
  transforming growth factor, alpha TGFA 2.79 0 1.54 14.86 AK312899
  wingless-type MMTV integration site family, member 6 WNT6 0.49 1.09 0.64 21.46 NM_006522
Antiviral immune response
  chemokine ligand 8 CCL8 8.02 0 3.17 0 NM_214214.1
  extracellular matrix protein 1 ECM1 2.01 0.54 2.89 0 CB477333
  IFN-gamma IFNG 0.49 0.41 3.18 0 NM_213948.1
  interleukin 18 IL18 2.58 0.95 5.84 19.25 NM_001562
  ISG15 ubiquitin-like modifier ISG15 1.56 10.92 2.51 0 EU584557.1
  interferon-stimulated gene 20 kDa protein ISG20 1.49 61.10 2.20 4.94 NM_002201
  vasoactive intestinal peptide VIP 0.69 32.11 4.14 0 NM_194435
Apoptosis
  BCL2/adenovirus E1B 19kDa interacting protein 3 BNIP3 3.69 0 2.61 2.88 U15174.1
  CD14 molecule CD14 3.60 0 3.87 0 NM_001097445
  immediate early response 3 IER3 5.46 0.41 2.21 1.64 NM_003897
  lectin, galactoside-binding, soluble, 1 LGALS1 0.42 0.82 0.66 10.51 NM_002305
  interleukin 1 alpha IL1A 21.31 0 8.47 0 NM_214029.1
  interleukin 1, beta IL1B 18.69 0 10.33 2.88 M15330.1
  serine/threonine kinase 17a STK17A 1.53 1.62 2 1.64 NM_00476
  tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain TNFRSF10D 2.26 0 2.21 61.11 NM_003840
  tumor necrosis factor alpha TNFα 5.13 0.41 1.96 6.28 EU682384.1
Cell proliferation
  Betacellulin BTC 2.26 0.95 1.78 1.97 NM_001729
  epithelial membrane protein 1 EMP1 0.49 0.82 0.62 2.88 NM_001423
  fatty acid binding protein 3, muscle and heart FABP3 1.88 0.95 2.57 3.09 NM_004102
  fms-related tyrosine kinase 1 FLT1 1.91 1.78 2.49 0 NM_002019
  interleukin 2 receptor, gamma IL2RG 1.39 6.28 2.06 1.07 NM_000206
  interleukin 8 receptor, beta IL8RB 1.33 45.16 3.41 0 NM_001557
  v-myc myelocytomatosis viral oncogene homolog MYC 0.75 14.04 0.29 0.71 NM_002467
  pro-platelet basic protein PPBP 2.75 0.95 3.57 1.97 NM_002704
  1. Note: The DE genes are presented with putative functions assigned by the GO term and manual annotation. Many genes with multiple functions were only listed in one category according to specific biology processes. FC: fold change; FC≥2: up-regulation (infection/control); FC≤0.5: down-regulation.
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