Table 2.
Genes upregulated in the brains of mice infected with T. gondii for a year
| Function | Gene* [Number/ID]† |
| Antibody | Ig heavy chain V regions [116] |
| Ig kappa V regions [119] | |
| Ig lambda 1 germline V region (Igl-V1, 1810027O01Rik, IgL) [V00811] | |
| Ig alpha chain (IGHV1S44) [M19402] | |
| Rearranged IgA-chain gene, V region (IGHV1S46) [M20774] | |
| IgG-1 gene, D-J-C region: 3' exon for secreted form (Igh-4, IgG1) [J00453] | |
| Ig germline D-J-C region alpha gene and secreted tail (Igh-VJ558, AI893585, MGC118142, MGC6727, Igh-A (1g2), Vh186.2/Jh2) [J00475] | |
| Ig gamma2a-b(c57bl/6 allele) c gene and secreted tail (IGHG2C) [J00479] | |
| Immunoglobulin joining chain (Igj, 9530090F24Rik, AI323815, Jch) [NM_152839] | |
| Antigen presentation | MHC-I Similar to H-2 MHC-I antigen, D-37 alpha chain precursor (C920025E04Rik) [AK083387] |
| MHC-I Transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) (Tap2, ABC18, AI462429, APT2, Abcb3, Ham-2, Ham2, MTP2, PSF2, RING11, Tap-2, Y1, jas) [NM_011530] | |
| MHC-II [22] | |
| MHC-III (D17H6S56E-3, C6orf27, G7c, NG37) [NM_138582] | |
| Beta-2 microglobulin (B2m, Ly-m11, beta2-m) [NM_009735] | |
| Complement | Complement component 4A/sex limited protein (C4a, Slp) GeneCards: Primarily expressed in liver and to a lesser extent in immune cells [NM_011413] |
| Complement component 4B (C4b, C4, Ss) [NM_009780] | |
| Complement component 1, r subcomponent (C1r, AI132558, C1rb) [NM_023143] | |
| Complement component C1SB (C1sb) [NM_173864] | |
| Complement component 1, q subcomponent, alpha polypeptide (C1qa, AI255395, C1q) [NM_007572] | |
| Complement component 1, q subcomponent, C chain (C1qc, AI385742, C1qg, Ciqc) [NM_007574] | |
| Major inhibitor of classical complement | Serine (or cysteine) peptidase inhibitor, clade G, member 1 (Serping1, C1INH, C1nh) [NM_009776] |
| Serine (or cysteine) peptidase inhibitor, clade A, member 3N (Serpina3n, Spi2-2, Spi2.2, Spi2/eb.4) GeneCards: Although its physiological function is unclear, it can inhibit neutrophil cathepsin G and mast cell chymase. [NM_009252] |
|
| GTPase | Interferon inducible GTPase 1 (Iigp1, 2900074L10Rik, AI046432, AW111922, Iigp) [AK013785] |
| Interferon inducible GTPase 1 (AW111922, Iigp1) [NM_021792] | |
| Interferon inducible GTPase 2 (Iigp2, RP24-499A8.1, AI481100, GTPI, (GC102455) [NM_019440] | |
| Interferon gamma inducible protein 47 (Ifi47, IRG-47, Iigp4, Iipg4, Olfr56) [NM_008330] | |
| Interferon gamma induced GTPase (Igtp, RP24-499A8.4, AW558444) [NM_018738] | |
| GTPase, IMAP family member 4 (Ian1, Gimap4, AU019574, E430007K16Rik, IMAP4, MGC11734, mIAN1), transcript variant 1 GeneCards: Exhibits intrisinic GTPase activity. [NM_174990] |
|
| Transcription | Signal transducer and activator of transcription (Stat1, 2010005J02Rik, AA408197) GeneCards: Mediates signaling by interferons. Results in induction of a cellular antiviral state. [NM_009283 BC057690] |
| Transcription factor MafB (v-maf musculoaponeurotic fibrosarcoma oncogene homolog B).(Mafb, Kreisler, Krml, kr) GeneCards: Plays a pivotal role in regulating lineage-specific hematopoiesis by repressing ETS1-mediated transcription of erythroid-specific genes in myeloid cells (By similarity). [NM_010658] |
|
| Down regulator of transcription 1/Differentially regulated in lymphoid organs and differentiation (Dr1d) [AF043513] | |
| Suppression of cytokine signaling | Suppressor of cytokine signaling 1 (Socs1, Cish1, Cish7, JAB, SOCS-1, SSI-1) GeneCards: SOCS1 is involved in negative regulation of cytokines that signal through the JAK/STAT3 pathway. Appears to be a major regulator of signaling by interleukin 6 (IL6) and leukemia inhibitory factor (LIF). Regulates interferon-gamma mediated sensory neuron survival (By similarity). [NM_009896] |
| Proteosome/antigen processing | Proteosome (prosome, macropain) subunit, beta type 8 (large multifunctional peptidase 7) (Psmb8, Lmp-7, Lmp7) GeneCards: This subunit is involved in antigen processing to generate class I binding peptides. Stimulated by interferon gamma, involved in the degradation of cytoplasmic antigens for MHC class I antigen presentation pathways. [NM_010724] |
| Proteosome (prosome, macropain) subunit, beta type 9 (large multifunctional peptidase 2) (Psmb9, Lmp-2, Lmp2) GeneCards: stimulated by interferon gamma, involved in the degradation of cytoplasmic antigens for MHC class I antigen presentation pathways. [NM_013585] | |
| Proteasome (prosome, macropain) 28 subunit, alpha (Psme1, AW413925, MGC113815, PA28a) GeneCards: Implicated in immunoproteasome assembly and required for efficient antigen processing. The PA28 activator complex enhances the generation of class I binding peptides by altering the cleavage pattern of the proteasome. Induction by interferon gamma. [NM_011189] |
|
| Antimicrobial | Secretory leukocyte peptidase inhibitor (Slpi) Acid-stable proteinase inhibitor with strong affinities for trypsin, chymotrypsin, elastase, and cathepsin G. Secretory leukoprotease inhibitor, involved in antineutrophil elastase protection at inflammatory sites. [NM_011414] |
| Defensin related cryptdin 17 (Defcr17, AU014719, Cryp17) GeneCards: Acid-stable proteinase inhibitor with strong affinities for trypsin, chymotrypsin, elastase, and cathepsin G. Secretory leukoprotease inhibitor, involved in antineutrophil elastase protection at inflammatory sites [S73391] |
|
| Pre-B-cell growth | Bone marrow stromal cell antigen 2 (Bst2, 2310015I10Rik, C87040, DAMP-1) GeneCards: May be involved in pre-B-cell growth. [NM_198095] |
| T lymphocyte proliferation | CD274 antigen/Programmed cell death 1 ligand 1 precursor (Cd274, B7-H1, PD-L1, Pdcd1l1, Pdcd1lg1) Genecards: Involved in costimulatory signal, essential for T lymphocyte proliferation and production of IL10 and IFNG, in an IL2-dependent and a PDCD1-independent manner. Interaction with PDCD1 inhibits T-cell proliferation and cytokine production. Up-regulated on T and B cells, dendritic cells, keratinocytes and monocytes after LPS and IFNG activation. Up-regulated in B cells activated by surface Ig cross-linking. [NM_021893] |
| Lymphocyte activation | Lymphocyte-activation gene 3 (Lag3, CD223, LAG-3, Ly66) GeneCards: Involved in lymphocyte activation. Binds to HLA class-II antigens. Highly homologous to CD4, expressed exclusively in activated T and NK lymphocytes, major MHC class 2 ligand potentially involved in the regulation of immune response. [NM_008479] |
| Macrophage growth | Guanylate nucleotide binding protein 2 (Gbp2) Uniprot: Interferon-induced Gbp 2 [NM_010260] |
| Guanylate nucleotide binding protein 4 (Gbp4, AW228655, Gbp3) [NM_018734] | |
| Macrophage activation 2/guanylate-binding protein 4 homolog (Mpa2, AW228052, Gbp4, KIAA4245, Mag-2, Mpa-2, mKIAA4245) [NM_008620] | |
| Macrophage activation 2 like (MPA2l, AI595338) [NM_194336] | |
| Guanylate nucleotide binding protein 5 (Gbp5, 5330409J06Rik) Uniprot: Interferon-induced Gbp5 [NM_153564] | |
| RIKEN cDNA 5830443L24 gene/guanylate binding protein 8(5830443L24Rik, mGBP8) [NM_029509] | |
| cDNA sequence BC057170/guanylate binding protein like (BC057170, E430029F06) [NM_172777] | |
| Immune response/binding | Interferon-induced protein with tetratricopeptide repeats 3 (Ifit3, Ifi49, MGC107331) [NM_010501] GO:0000004 biological process unknown GO:0005488 binding GO:0005554 molecular function unknown GO:0006955 immune response GO:0008372 cellular component unknown |
| Astrocyte protein after trauma | Glial fibrillary acidic protein (Gfap, AI836096) GeneCards: Class-III intermediate filament, cell-specific marker; during development of CNS distinguishes astrocytes from other glial cells. Almost exclusively expressed in astrocytes; interacts with S100A1. S100A1 home page: S100A1 and S100B can be isolated as a complex from bovine brain; mixture of S100A1 and S100B inhibited the assembly of tubulin into microtubules [NM_010277] |
| Chemo-attractants | Chemokine (C-C motif) ligand 5 (Ccl5, MuRantes, RANTES, SISd, Scya5, TCP228) GeneCards: Chemoattractant for blood monocytes, memory T helper cells and eosinophils. [NM_013653] |
| Chemokine (C-C motif) ligand 8/monocyte chemoattractant protein-2 precursor (Ccl8, RP23-446K18.1, 1810063B20Rik, AB023418, HC14, MCP-2, Mcp2, Scya8) GeneCards: Interferon gamma induced chemotaxis Attracts monocytes, lymphocytes, basophils, eosinophils [NM_021443] |
|
| Cell adhesion/interaction | CD36 antigen/fatty acid translocase (Cd36, FAT, GPIV, Scarb3) May function as a cell adhesion molecule. GeneCards: Directly mediates cytoadherence of Plasmodium falciparum parasitized erythrocytes. Mediates free radical production in cerebral ischemia. Publication (Khoury, J Exp Med 2003, 197(12) 1657–1666): CD36, a major pattern recognition receptor, mediates microglial and macrophage response to beta-amyloid, and imply that CD36 plays a key role in the proinflammatory events associated with Alzheimer's disease. [NM_007643] |
| EGF-like module containing, mucin-like, hormone receptor-like sequence 1/cell surface glycoprotein F4/80/lymphocyte antigen 71 (Emr1, D7A5-7, EGF-TM7, F4/80, Gpf480, Ly71, TM7LN3) GeneCards: Could be involved in cell-cell interactions. [NM_010130] |
|
| Lectin, galactoside-binding, soluble, 3 binding protein/cyclophilin associated. protein (Lgals3bp, 90K, CyCAP, MAC-2BP, Ppicap) GeneCards: Promotes integrin-mediated cell adhesion. May stimulate host defense against viruses and tumor cells. [NM_011150] |
|
| Leukocyte integrin/actin signaling | FYN binding protein (Fyb, ADAP, B630013F22Rik) GeneCards: Acts as an adapter protein of the FYN and SH2-domain-containing leukocyte protein-76 (SLP76) signaling cascades in T cells. Modulates expression of interleukin-2 (IL-2). [NM_011815] |
| Free radical production | Cytochrome b-245, beta polypeptide (Cybb, C88302, Cgd, Nox2, gp91<phox>, gp91phox) GeneCards: Critical component of the membrane-bound oxidase of phagocytes that generates superoxide. [NM_007807] |
| Apoptosis retardation | B-cell leukemia/lymphoma 2 related protein A1c(Bcl2a1, A1-c c) GeneCards: Retards apoptosis induced by IL-3 deprivation. May function in response of hemopoietic cells to external signals and in maintaining endothelial survival during infection (By similarity). [NM_007535] |
| ADP ribosylation | Poly (ADP-ribose) polymerase family, member 14/collaborator of STAT6 (Parp14, 1600029O10Rik, BC021340, KIAA1268, MGC29390, mKIAA1268) [BC021340] |
| Unknown | [XM_207778] |
* Gene names and symbols from Entrez Gene [87] and function information from GeneCards [88]
†Either the number of genes in this category or the accession number
Function of all genes significantly upregulated in the brains of mice infected with T. gondii for a year (p-value after adjustment for multiple testing < 0.01). No genes were significantly downregulated. Gene names and symbols were retrieved from Entrez Gene [87] using the accession number and function information from GeneCards [88]. Each distinct gene symbol is included in the column headed Gene, except for the functions Antibody and Antibody presentation, where there were too many similar accession numbers. The Number/ID is in brackets contains the accession number where there were < 4 for a function or else a count of the accession numbers for that function.