Table 2.
Differential expressed mRNAs detected by microarray analysis at 3 dpi
| ID (#) | Fold changea | Blastn or tblastxb | Tentative function (functional cluster)c | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Spleen | Lymph node | Tonsil | |||||||||||
| LV | MV | HV | LV | MV | HV | LV | MV | HV | Gene name or tentative annotation (T[H]C) | Acc. number | E-value (nt) | ||
| Higher in infected | |||||||||||||
| CSF-1 | – | – | – | 4.0 | – | – | – | – | – | Allograft inflammatory factor 1 (AIF1) | XM_001490247 | 4E-154 (474) | Growth-suppressing (IFN-γ) |
| CSF-2 | – | – | – | 3.8 | – | – | – | – | – | IFN-gamma-inducible protein 16, transcript variant 1 (IFI16), mRNA | ref|XM-001170179.1| | 4E-47 (656) | Growth-suppressing (IFN-γ) |
| CSF-3 (2) | – | – | – | 4.2 | – | – | – | – | – | Guanylate binding protein 2 (interferon-inducible) (GBP2), mRNA | ref|NM-004120. | 1E-123 (711) | Signal transduction/antiviral effect (IFN-γ) |
| CSF-4 | – | – | – | 3.5 | 4.6 | – | – | – | – | Similar to dendritic cell-derived IFNG-induced monocyte protein 5 (MOP5) | pig|TC265382 | 2E-54 (432) | Metal dependent phosphohydrolase (IFN-γ) |
| CSF-5 | – | – | – | 3.5 | – | 4.8 | – | – | – | Polyubiquitin, transcript variant 12 (UBC), mRNA | XM_874550.3 | 0 (790) | Component proteasome (UMP) |
| CSF-6 | – | 5.3 | 5.0 | – | – | – | – | – | – | Proteasome (prosome, macropain) subunit alpha type, 6 (Psma6) mRNA | NM_002791 | 0 (658) | Component proteasome (UMP) |
| CSF-7 (3) | 5.6 | 5.7 | 6.1 | 5.3 | 5.1 | – | 5.3 | 5.4 | 6.0 | HECT domain and RCC1-like domain-containing protein 6 (HERC6) | Pig|TC273610 | 2.9E-121 (715) | Potential ubiquitin ligase (UMP) |
| CSF-8 (2) | 4.6 | 5.7 | 5.9 | 4.3 | 5.7 | – | 3.9 | 5.4 | 4.6 | Similar to poly (ADP-ribose) polymerase family, member 14, mRNA (BAL2) | BC120371 | 5E-179 (626) | DNA-damage induced/cell survival (UMP/Apopt.) |
| CSF-9 (2) | – | 5.5 | 6.0 | – | – | – | – | 5.7 | 5.1 | Similar to HUMAN (Q9H0J9) Poly [ADP-ribose] polymerase 12 (PARP12) | pig|TC260164 | 2E-101(752) | DNA-damage induced/cell survival (UMP/Apopt.) |
| CSF-10 | – | 4.7 | 4.9 | – | – | – | – | – | – | Poly (ADP-ribose) polymerase family, member 9 (PARP9)(BAL1), mRNA | NM_001076828. | 2E-165 (817) | DNA-damage induced/cell survival (UMP/Apopt.) |
| CSF-11 | 7.2 | 6.8 | 9.9 | 6.3 | – | – | – | – | – | Similar to HCV-associated microtubular aggregate protein p44 (IFI44) | THC2463234 | 2.9E-23 (534) | Antiproliferative activity (IFN-α/β) |
| CSF-12 | 39 | 49 | 38 | 40 | 39 | 41 | 27 | 45 | 38 | CXC-like protein gene, complete cds (CXCL10/IP10) | AY894692. | 0 (533) | Pleiotropic cytokine (IFN-α/β) |
| CSF-13 | 21 | 23 | 18 | 14 | 13 | 13 | 18 | 25 | 24 | 2′–5′ oligoadenylate synthetase 2 (OAS2) | ref|NM-001031796.1| | 2E-136 (309) | dsRNA mediated antiviral response (IFN-α/β) |
| CSF-14 | 6.0 | 7.7 | 7.1 | 3.7 | 5.2 | – | – | 5.8 | 4.6 | TNF-related apoptosis-inducing ligand (TRAIL) mRNA | ref|NM-001024696.1| | 0 (1004) | Cytokine TNF ligand family (Apopt.) |
| CSF-15 | – | 5.8 | 6.5 | – | 6.0 | 10.2 | – | 7.2 | 4.4 | EST weakly similar to HUMAN (Q7Z5U7) cathepsin C (CTSC) | human|THC2686463 | 0.22 (276) | Lysosomal cysteine proteinase/requires Cl− (Apopt.) |
| CSF-16 | – | 4.0 | 6.0 | 4.4 | – | – | – | – | – | Similar to NADH-ubiquinone oxidoreductase chain 1 (NADH1) | ref|XM-001113286.1| | 6e-81(374) | Subunit mitochondrial complex I (Apopt.) |
| CSF-17 | – | – | – | 4.4 | 4.0 | – | – | – | – | Myeloid cell leukemia sequence 1 (MCL1)(BCL2-related) | ref|NM-021960.3| | 3E-136 (671) | Cell survival/anti-apoptotic (Apopt.) |
| CSF-18 | 12 | 18 | 13 | 12 | 9.4 | – | 11 | 15 | 14 | Glutamate-cysteine ligase, modifier subunit (GCLM), mRNA | ref|NM-199845.1| | 5E-29 (244) | Key enzyme glutathion metabolism (Apopt.) |
| CSF-19 (3) | – | 5.6 | 6.3 | 4.0 | 5.8 | 8.7 | – | 6.4 | 5.0 | Glutaredoxin (thioltransferase) (GLRX), mRNA | ref|NM-001037604.1| | 7e-51 (611) | Cell redox homeostasis/deglutathionylation (Apopt.) |
| CSF-20 | – | 5.1 | 6.6 | 5.9 | 5.9 | – | – | – | – | Calbindin D-9 k mRNA | NM_214140. | 1E-174 (516) | Calcium binding and transport activity (Apopt.) |
| CSF-21 | 3.6 | – | – | – | – | – | – | – | – | Sus scrofa MHC class I antigen 1 (SLA-1), mRNA | ref|NM-001097431.1| | 1E-86 (255) | Antigen presentation MHC I (Innate immune AP) |
| CSF-22 | – | – | – | – | – | – | – | 3.5 | – | Beta-2-microglobulin (B2 M), mRNA | ref|NM-004048.2| | 1E-26 (476) | Antigen presentation MHC I (Innate immune AP) |
| CSF-23 | – | – | – | – | – | – | – | 3.9 | – | Fc fragment of IgG, low affinity IIIb, receptor (CD16b) | ref|NM-214391.1| | 0 (794) | Natural killer cell mediated cytotoxicity (Innate Immune–AP) |
| CSF-24 (7) | – | – | – | 4.5 | 4.2 | – | – | – | – | Immunoglobulin J chain | ref|XM-001105782 | 8e-98 (348) | Joining IgM and IgA monomers (Adapt. Immune–AP) |
| CSF-25 (2) | – | – | – | 3.8 | 3.7 | – | – | – | – | Immunoglobulin lambda-chain (CD179b antigen) | ref|XM-850728.1| | 2e-96 (677) | Pre- B or T cell receptor (Adapt. Immune–AP) |
| CSF-26 (5) | – | – | – | 3.9 | 4.2 | – | – | – | – | Kappa light chain mRNA | ref|NM-001093783.1| | 1E-77 (494) | Pre- B or T cell receptor (Adapt. Immune–AP) |
| CSF-27 (2) | – | – | – | 3.7 | – | – | – | – | – | Immunoglobulin mu heavy chain constant region, mRNA | gb|S42881.1| | 0 (661) | Pre- B or T cell receptor (Adapt. immune–AP) |
| CSF-28 (2) | – | 3.8 | – | – | – | – | – | – | – | Placenta-specific 8 (PLAC8), mRNA | NM_016619. | 3e-59 (330) | Expressed in neutrophils/cell survival (Apopt ?) |
| CSF-29 | – | 3.8 | – | – | – | – | – | – | – | Sterile alpha motif domain containing 9 (SAMD9) | XM_001492397 | 2e-170 (595) | Cell proliferation (Apopt. ?) |
| CSF-30 | – | – | 4.6 | – | – | – | – | – | – | Similar to frizzled 5 (LOC710796), mRNA (FZD5) | ref|XR-012291.1| | 2e-12 (418) | Receptor for Wnt signaling proteins |
| CSF-31 | 4.5 | 4.5 | 4.5 | 5.3 | 4.7 | – | – | 5.5 | – | EST weakly similar to myelin expression factor 2 (MyEF2) | human|THC2606750 | 0.00012 (547) | Myocyte transcription enhancer |
| CSF-32 | – | 5.5 | 6.0 | – | 4.9 | – | – | – | – | Ribosomal protein L9 homologue (RPL9) | XM_001149849 | 7E-160 (790) | Structural component ribosome |
| CSF-33 | – | 4.1 | 4.9 | – | – | – | – | – | – | Chloride intracellular channel 5 (CLIC5), transcript variant 2, mRNA | ref|NM-016929.3| | 5e-40 (564) | Voltage-gated chloride channel (cytoskeleton) |
| Lower in infected | |||||||||||||
| CSF-34 | – | 0.16 | 0.18 | – | – | – | – | – | – | Actin, alpha 2, smooth muscle, aorta (ACTA2), mRNA | ref|NM-001034502.1| | 9e-76 (237) | Component cytoskeleton (cytoskeleton) |
| CSF-35 | – | 0.20 | 0.22 | – | – | – | – | – | – | Tropomyosin, transcript variant 25 (TPM1), mRNA | ref|XM-860199.1| | 5e-167 (623) | Component cytoskeleton (cytoskeleton) |
| CSF-36 (7) | – | 0.29 | – | 0.12 | 0.13 | 0.16 | – | – | – | Tblastx; mRNA clone:LVRM10070B07 homologue to B. taurus elastin | dbj|AK233022.1| | 0 (613) | Extracellular fibre |
| CSF-37 (4) | – | – | – | 0.09 | 0.07 | 0.11 | – | – | – | Complement component 4 binding protein, alpha (C4BPA)(APOR), mRNA | ref|NM-213942.1| | 0.0 (537) | Complement cascades (innate and adapt immune–AP) |
| CSF-38 (6) | – | – | – | 0.14 | 0.17 | – | – | – | – | Beta globin mRNA | ref|XM-537902.2| | 5e-172 (565) | Oxygen transport (Ox-P) |
| CSF-39 | – | – | – | 0.24 | – | – | – | – | – | Hemoglobin alpha chain | ref|NM-001077422.2| | 4e-117 (593) | Oxygen transport (Ox-P) |
| CSF-40 (2) | – | – | – | 0.25 | – | – | – | – | – | Solute carrier family 40 member 1 (Ferroportin 1), mRNA | XM_001250723 | 6e-87 (388) | Cellular iron ion homeostasis (Ox-P) |
| CSF-41 (3) | – | 0.23 | 0.21 | – | – | – | – | 0.27 | 0.22 | Cytochrome b (CYTB) | ref|NP-008646.1 | 1E-54 (434) | Oxidative phosphorylation (Ox-P) |
| CSF-42 | – | 0.29 | 0.29 | – | – | – | – | – | – | EST homoloque to NADH dehydrogenase subunit 4L (ND4L) | pig|TC238572 | 1.0e-18 (468) | Oxidative phosphorylation (Ox-P) |
| CSF-43 | – | – | 0.28 | – | – | – | – | – | 0.23 | Blastx; NADH dehydrogenase subunit 6 (ND6) | ref|NP-008645.1 | 3e-50 (524) | Oxidative phosphorylation (Ox-P) |
| CSF-44 | – | – | 0.23 | – | – | – | – | – | – | Ectonucleotide pyrophosphatase/phosphodiesterase 3 (ENPP3/CD203c) | ref|NM-001075923. | 0.0 (670) | Hydrolysis of Flavin adenine dinucleotide (Ox-P) |
aFold change; ratio of differential expression (infected over uninfected) of library probes (ID). The number of library probes (#) aligning to an identical accession number and also hybridizing differentially is given in parentheses behind the ID. For these sets of identical probes an average fold change was calculated
bDNA sequences of array probes were compared with the NCBI RNA reference sequence, NCBI non-redundant (nr), or the DFCI EST databases using blastn (or tblastx when indicated) and WU-BLAST 2.0 blast(n), respectively. Gene names or annotations of tentative consensus sequences (T[H]C), which scored the highest degree of homology, i.e., lowest E-value, are listed with their accession or T[H]C numbers (acc. number). The length of the probe-sequence (nt) compared is given in parenthesis behind the E-value. Based on data mining in the NCBI (Pub Med, Gene, OMIM, Unigene, conserved domain), HRPD, KEGG, Reactome, and BioCarta (pathway) databases a tentative function and/or process was assigned, and genes were clustered
cBased on data mining in the NCBI (Pub Med, Gene, OMIM, Unigene, conserved domain), HRPD, KEGG, Reactome, and BioCarta (pathway) databases a tentative function was assigned and functional cluster: (Apopt.), related to apoptosis. (IFN) IFN-α/β or γ induced. (Innate/adapt. immune-AP) adaptive and innate immune response including antigen presentation. (UBM), related to the proteosome pathway, i.e., ubiquitin-mediated proteolysis. (Cytoskeleton) components of, or proteins associated with the cytoskeleton. (Ox-P), involved in oxidative phosphorylation and oxygen transport