Table 1.
Genes from the innate immune response included in the gene sets used for analysis: complement cascade, cytokine response, chemokine response, toll-like receptor (TLR) cascade, and pattern recognition receptors (PRRs).
| Gene symbol | Gene name | Role in the Immune Response |
|---|---|---|
| AIM2 | Interferon Inducible protein | Pattern recognition receptors |
| Atm | ataxia telangiectasia mutated | NFκB pathway |
| Bcl10 | B cell leukemia/lymphoma 10 | NFκB pathway |
| Bcl2 | B cell leukemia/lymphoma 2 | NFκB pathway |
| Bcl2a1a | B cell leukemia/lymphoma 2 related protein A1a | NFκB pathway |
| Bcl2l1 | BCL2-like 1 | NFκB pathway |
| Birc2 | baculoviral IAP repeat-containing 2 | Cytokine response, NFκB pathway, TLR pathway |
| Birc3 | baculoviral IAP repeat-containing 3 | Cytokine response |
| Blnk | B cell linker | NFκB pathway |
| Btk | Bruton agammaglobulinemia tyrosine kinase | NFκB pathway |
| C1qa | complement component 1, q subcomponent, α polypeptide | Complement and coagulation |
| C1qb | complement component 1, q subcomponent, β polypeptide | Complement and coagulation |
| C1qc | complement component 1, q subcomponent, C chain | Complement and coagulation |
| C3 | complement component 3 | Complement and coagulation |
| C3ar1 | complement component 3a receptor 1 | Complement and coagulation |
| C5ar1 | complement component 5a receptor 1 | Complement and coagulation |
| Casp1 | caspase 1 | Cytokine response |
| Casp3 | caspase 3 | Cytokine response |
| Casp8 | caspase 8 | TLR pathway |
| Cd14 | CD14 antigen | Pattern recognition receptors, TLR pathway, NFκB pathway |
| Cd36 | CD36 molecule | TLR pathway |
| Cd45 | CD45 antigen | Cellular markers |
| Cd68 | CD68 antigen | Cellular markers |
| Cflar | CASP8 and FADD-like apoptosis regulator | NFκB pathway |
| Chuk | conserved helix-loop-helix ubiquitous kinase | Cytokine response, NFκB pathway, TLR pathway |
| Csf1 | colony stimulating factor 1 (macrophage) | Cytokine response |
| Csf1r | colony stimulating factor 1 receptor | Cytokine response |
| Csf2rb | colony stimulating factor 2 receptor, β, low-affinity (granulocyte-macrophage) | Cytokine response |
| Ctss | cathepsin S | TLR pathway |
| Ddx58 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 | Cytokine response, NFκB pathway |
| Dusp7 | dual specificity phosphatase 7 | Cytokine response, TLR pathway |
| F3 | coagulation factor III | Complement and coagulation |
| Fos | FBJ osteosarcoma oncogene | Cytokine response, TLR pathway |
| GFAP | glial fibrillary acidic protein | Cellular markers |
| Fyn | Fyn proto-oncogene | Cytokine response |
| Hmgb1 | high mobility group box 1 | Cytokine response, TLR pathway |
| Ifnar1 | interferon (α and β) receptor 1 | Cytokine response |
| Ifnar2 | interferon (α and β) receptor 2 | Cytokine response |
| Ikbkb | inhibitor of kappaB kinase β | Cytokine response, NFκB pathway, TLR pathway |
| Ikbkg | inhibitor of kappaB kinase gamma | NFκB pathway |
| Il10rb | interleukin 10 receptor, β | Cytokine response |
| Il1a | interleukin 1 α | Cytokine response |
| Il1b | interleukin 1 β | NFκB pathway |
| Il1r1 | interleukin 1 receptor, type I | NFκB pathway |
| Il1rap | interleukin 1 receptor accessory protein | Cytokine response |
| Il2rg | interleukin 2 receptor, gamma chain | Cytokine response |
| Il6ra | interleukin 6 receptor, a | Cytokine response |
| Inpp5d | inositol polyphosphate-5-phosphatase D | Cytokine response |
| Irak1 | interleukin-1 receptor-associated kinase 1 | Cytokine response, NFκB pathway, TLR pathway |
| Irak2 | interleukin-1 receptor-associated kinase 2 | Cytokine response, TLR Pathway |
| Irak4 | interleukin-1 receptor-associated kinase 4 | Cytokine response, NFκB pathway, TLR pathway |
| Irf3 | interferon regulatory factor 3 | Cytokine response, TLR pathway |
| Irf7 | interferon regulatory factor 7 | TLR pathway |
| Itgam | integrin α M | Pattern recognition receptors, Complement and coagulation, TLR pathway |
| Jun | jun proto-oncogene | Cytokine response, TLR pathway |
| Lgmn | legumain | TLR pathway |
| Ltbr | lymphotoxin B receptor | Cytokine response, NFκB pathway |
| Lyn | LYN proto-oncogene, Src family tyrosine kinase | NFκB pathway |
| Map2k4 | mitogen-activated protein kinase 4 | Cytokine response, TLR pathway |
| Map3k1 | mitogen-activated protein kinase 1 | TLR pathway |
| Map3k14 | mitogen-activated protein kinase 14 | Cytokine response |
| Mapk10 | mitogen-activated protein kinase 10 | Cytokine response, TLR pathway |
| Mapk14 | mitogen-activated protein kinase 14 | Cytokine response, TLR pathway |
| Myd88 | myeloid differentiation primary response gene 88 | Cytokine response, NFκB pathway, TLR pathway |
| NFκB1 | nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105 | Cytokine response, NFκB pathway, TLR pathway |
| NFκB2 | nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100 | Cytokine response |
| NFκBia | nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, α | Cytokine response, NFκB pathway, TLR pathway |
| Nod1 | nucleotide-binding oligomerization domain containing 1 | Cytokine response, Pattern recognition receptors, TLR pathway |
| Osmr | oncostatin M receptor | Cytokine response |
| Parp1 | poly (ADP-ribose) polymerase family, member 1 | NFκB pathway |
| Pik3ca | phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α | Cytokine response |
| Pik3cb | phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit β | Cytokine response |
| Pik3r2 | phosphoinositide-3-kinase regulatory subunit 2 | Cytokine response |
| Plcg2 | phospholipase C, gamma 2 | NFκB pathway, TLR pathway |
| Prkaca | protein kinase, cAMP dependent, catalytic, α | Cytokine response |
| Prkcq | protein kinase C, theta | NFκB pathway |
| Pros1 | protein S (α) | Complement and coagulation |
| Psmb8 | proteasome (prosome, macropain) subunit, β type 8 (large multifunctional peptidase 7) | Cytokine response |
| Ptgs2 | prostaglandin-endoperoxide synthase 2 | NFκB pathway |
| Ptpn6 | protein tyrosine phosphatase, non-receptor type 6 | Cytokine response |
| RAGE | receptor for advanced glycation endproducts | Pattern recognition receptors |
| Rela | v-rel reticuloendotheliosis viral oncogene homolog A (avian) | Cytokine response, NFκB pathway, TLR pathway |
| Relb | avian reticuloendotheliosis viral (v-rel) oncogene related B | Cytokine response, NFκB pathway |
| Rig-1 | retinoic acid-inducible gene I | Pattern recognition receptors |
| Ripk1 | receptor (TNFRSF)-interacting serine-threonine kinase 1 | NFκB pathway, TLR pathway |
| Ripk2 | receptor (TNFRSF)-interacting serine-threonine kinase 2 | Cytokine response, TLR pathway |
| S100b | S100 protein, β polypeptide, neural | Cytokine response, TLR pathway |
| Serpine1 | serine (or cysteine) peptidase inhibitor, clade E, member 1 | Complement and coagulation |
| Smarca4 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 | Cytokine response |
| Sqstm1 | sequestosome 1 | Cytokine response |
| Stat1 | signal transducer and activator of transcription 1 | Cytokine response |
| Sumo1 | small ubiquitin-like modifier 1 | Cytokine response |
| Syk | spleen tyrosine kinase | Cytokine response, NFκB pathway |
| Tlr2 | toll-like receptor 2 | Pattern recognition receptors, TLR pathway |
| Tnfrsf12a | tumor necrosis factor receptor superfamily, member 12a | Cytokine response |
| Tnfrsf1a | tumor necrosis factor receptor superfamily, member 1a | Cytokine response, NFκB pathway |
| Tnfrsf1b | tumor necrosis factor receptor superfamily, member 1b | Cytokine response |
| Tnfrsf25 | tumor necrosis factor receptor superfamily, member 25 | Cytokine response |
| Tnfsf12 | tumor necrosis factor (ligand) superfamily, member 12 | Cytokine response |
| Traf2 | TNF receptor-associated factor 2 | Cytokine response, NFκB pathway |
| Traf3 | TNF receptor-associated factor 3 | Cytokine response, NFκB pathway, TLR pathway |
| Traf6 | TNF receptor-associated factor 6 | Cytokine response, NFκB pathway, TLR pathway |
| Vamp7 | vesicle-associated membrane protein 7 | Cytokine response |
| Vav1 | vav 1 oncogene | Cytokine response |
| Xiap | X-linked inhibitor of apoptosis | NFκB pathway |