Table-1.
Immune response genes regulated by SV40, TAg and mutants.
| Specific Function Biological Process Description | Entrez Gene ID | Gene Symbol | SV40 | TAg | N136 | 3213 | D44N | ||
|---|---|---|---|---|---|---|---|---|---|
| Transcription | Interferon type I biosynthetic process | interferon regulatory factor 7 | 54123 | Irf7 | 29.1 | 4.2 | 1.0 | 0.8 | 5.7 |
| interferon dependent positive acting transcription factor 3 gamma | 16391 | Irf9 | 3.7 | 2.8 | 0.9 | 0.7 | 2.4 | ||
| JAK/Stat signaling | signal transducer and activator of transcription 1 | 20846 | Stat1 | 5.8 | 3.1 | 1.5 | 0.5 | 2.0 | |
| signal transducer and activator of transcription 2 | 20847 | Stat2 | 7.5 | 1.9 | 1.0 | 0.5 | 1.5 | ||
| Cytokine and chemokine signaling | N-myc (and STAT) interactor | 64685 | Nmi | 3.5 | 4.3 | 1.4 | 1.2 | 2.3 | |
| PML body | promyelocytic leukemia | 18854 | Pml | 1.8 | 2.5 | 3.1 | 1.4 | 1.9 | |
| nuclear antigen Sp100 | 20684 | Sp100 | 4.5 | 7.2 | 1.1 | 1.1 | 2.2 | ||
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| RNA binding | Interferon-induced | 2'-5' oligoadenylate synthetase 1C | 114643 | Oas1c | 2.5 | 2.4 | 2.2 | 1.5 | 2.5 |
| 2'-5' oligoadenylate synthetase-like 1 | 231655 | Oasl | 16.0 | 2.7 | 1.2 | 1.1 | 3.5 | ||
| 2'-5' oligoadenylate synthetase 1A | 246730 | Oas1a | 13.8 | 18.9 | 4.0 | 1.3 | 15.1 | ||
| 2'-5' oligoadenylate synthetase 2 | 246728 | Oas2 | 9.5 | 9.1 | 2.1 | 1.2 | 4.2 | ||
| 2'-5' oligoadenylate synthetase-like 2 | 23962 | Oasl2 | 82.4 | 16.3 | 0.6 | 0.4 | 7.1 | ||
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| Binding to other proteins | Interferon-induced | interferon-induced protein with tetratricopeptide repeats 1 | 15957 | Ifit1/ISG56 | 55.7 | 7.7 | 2.0 | 0.5 | 4.6 |
| interferon-induced protein with tetratricopeptide repeats 2 | 15958 | Ifit2 / ISG54 | 4.3 | 2.4 | 1.7 | 0.9 | 2.1 | ||
| interferon-induced protein with tetratricopeptide repeats 3 | 15959 | Ifit3 / ISG49 | 13.5 | 4.3 | 1.1 | 0.4 | 3.0 | ||
| interferon activated gene 202B | 26388 | Ifi202b | 7.7 | 3.3 | 1.2 | 0.8 | 2.3 | ||
| interferon activated gene 203 | 15950 | Ifi203 | 10.8 | 2.7 | 1.2 | 1.0 | 2.0 | ||
| interferon activated gene 204 | 15951 | Ifi204 | 8.3 | 3.2 | 0.9 | 1.1 | 1.8 | ||
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| NC* | Interferon-induced | interferon-induced protein 35 | 70110 | Ifi35 | 3.6 | 3.1 | 1.8 | 1.0 | 2.1 |
| interferon-induced protein 44 | 99899 | Ifi44 | 49.8 | 17.0 | 1.1 | 0.5 | 6.5 | ||
| interferon, alpha-inducible protein 27 | 76933 | Ifi27 | 21.6 | 21.5 | 3.4 | 1.6 | 6.5 | ||
| interferon gamma inducible protein 47 | 15953 | Ifi47 | 9.0 | 4.2 | 0.9 | 0.9 | 1.9 | ||
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| Helicase | Interferon-induced | interferon induced with helicase C domain 1 | 71586 | Ifih1 | 22.6 | 8.9 | 3.0 | 0.6 | 4.7 |
| Interferon type I biosynthetic process | DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 | 230073 | Ddx58 / RIG-I | 5.5 | 4.2 | 1.2 | 0.9 | 1.6 | |
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| Catalytic activity | Virus response | radical S-adenosyl methionine domain containing 2 | 58185 | Rsad2 | 37.9 | 12.4 | 1.5 | 1.2 | 6.7 |
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| GTPase | Interferon-induced | myxovirus (influenza virus) resistance 1 | 17857 | Mx1 | 11.4 | 4.1 | 1.1 | 0.9 | 1.8 |
| myxovirus (influenza virus) resistance 2 | 17858 | Mx2 | 8.0 | 3.2 | 0.9 | 1.0 | 2.5 | ||
| GTPase, very large interferon inducible 1 | 74558 | Gvin1 | 3.4 | 2.5 | 1.7 | 0.5 | 1.1 | ||
| interferon inducible GTPase 1 | 60440 | Iigp1 | 23.2 | 6.8 | 0.3 | 0.3 | 2.8 | ||
| interferon inducible GTPase 2 | 54396 | Iigp2 | 10.1 | 8.5 | 1.0 | 0.6 | 4.4 | ||
| interferon gamma induced GTPase | 16145 | Igtp | 15.0 | 8.1 | 1.7 | 0.8 | 4.0 | ||
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| Protein Kinase | Interferon-induced | eukaryotic translation initiation factor 2-alpha kinase 2 | 19106 | Eif2ak2 / PKR | 3.1 | 2.3 | 1.1 | 0.9 | 2.0 |
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| ubiquitin like/protein binding | Interferon-induced | interferon, alpha-inducible protein | 100038882 | Isg15 | 33.2 | 9.8 | 1.7 | 0.4 | 4.1 |
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| Exonulcease | Interferon-induced | interferon-stimulated protein | 57444 | Isg20 | 3.8 | 1.9 | 1.1 | 1.6 | 1.8 |
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| Adenosine Deaminase | Interferon-induced | adenosine deaminase, RNA-specific | 56417 | Adar | 5.2 | 5.0 | 1.8 | 0.9 | 2.5 |
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| Receptor | Response to microbial infections | toll-like receptor 3 | 142980 | Tlr3 | 3.4 | 3.9 | 1.8 | 1.1 | 2.6 |
| Cell adhesion | lectin, galactose binding, soluble 9 | 16859 | Lgals9 | 3.5 | 3.9 | 0.9 | 1.1 | 2.4 | |
| Cell proliferation | CD274 antigen | 60533 | Cd274 | 2.4 | 2.6 | 1.3 | 1.3 | 1.2 | |
| Interferon-induced | RIKEN cDNA 5830458K16 gene | 67775 | Rtp4 | 28.3 | 7.4 | 1.6 | 0.4 | 4.3 | |
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| Endopeptidase | Antigen presentation | proteosome (prosome, macropain) subunit, beta type 8 (large multifunctional peptidase 7) | 16913 | Psmb8 | 10.6 | 5.5 | 1.5 | 0.4 | 2.6 |
| proteosome (prosome, macropain) subunit, beta type 9 (large multifunctional peptidase 2) | 16912 | Psmb9 | 4.1 | 6.3 | 3.6 | 0.6 | 2.4 | ||
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| MHC class II presentation | Antigen presentation | Ia-associated invariant chain | 16149 | Cd74 | 1.1 | 2.1 | 0.8 | 1.9 | 1.4 |
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| MHC class I presentation | Antigen presentation | histocompatibility 2, K1, K region | 14972 | H2-K1 | 6.1 | 4.5 | 2.0 | 1.6 | 3.4 |
| histocompatibility 2, D region locus 1 | 14964 | H2-D1 | 3.5 | 4.2 | 3.0 | 1.5 | 2.5 | ||
| histocompatibility 2, K1, K region | 100044874 | LOC1000 44874 | 6.9 | 5.2 | 2.0 | 1.8 | 3.9 | ||
| histocompatibility 2, T region locus 23 | 15040 | H2-T23 | 5.1 | 3.6 | 3.0 | 0.9 | 2.0 | ||
| histocompatibility 2, D region locus 1 | 14980 | H2-L | 2.4 | 2.2 | 1.6 | 0.9 | 1.5 | ||
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| GTP binding | Interferon-induced | guanylate nucleotide binding protein 2 | 14469 | Gbp2 | 11.7 | 2.8 | 1.8 | 0.5 | 1.6 |
| macrophage activation 2 like | 100702 | Mpa2l | 18.3 | 8.5 | 0.8 | 0.6 | 3.1 | ||
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| transferase activity | protein localization | poly (ADP-ribose) polymerase family, member 9 | 80285 | Parp9 | 5.3 | 4.0 | 1.2 | 0.5 | 2.3 |
| Virus response | zinc finger CCCH type, antiviral 1 | 78781 | Zc3hav1 | 3.8 | 2.8 | 1.0 | 1.2 | 2.1 | |
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| cyclic-nucleotide phosphodiesterase activity | IFN-induced | SAM domain and HD domain, 1 | 56045 | Samhd1 | 2.5 | 2.3 | 1.4 | 1.8 | 2.0 |
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| dTTP biosynthesis | LPS response | thymidylate kinase family LPS-inducible member | 22169 | Tyki | 39.6 | 8.5 | 0.7 | 0.8 | 4.6 |
| placenta-specific 8 | 231507 | Plac8 | 11.9 | 2.0 | 0.1 | 0.5 | 0.3 | ||
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| phospholipid binding | defense response | lymphocyte antigen 6 complex, locus E | 17069 | Ly6e | 3.5 | 2.3 | 1.1 | 1.7 | 1.4 |
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| Ubiquitin ligase | Interferon-induced | deltex 3-like (Drosophila) | 209200 | Dtx3l | 6.5 | 3.7 | 1.3 | 0.7 | 2.6 |
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| Peptidase | Interferon-induced | ubiquitin specific peptidase 18 | 24110 | Usp18 | 49.0 | 20.4 | 1.8 | 0.7 | 9.7 |
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| Protein/nucleic acid binding | Interferon-induced | tripartite motif protein 34 | 94094 | Trim34 | 3.4 | 2.2 | 1.2 | 0.8 | 0.9 |
List of selected immune response genes showing differential regulation (in fold change) by SV40, TAg and mutants compared to wild-type MEFs.
NC* = Not classified.