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Table 2 Genes upregulated in the brains of mice infected with T. gondii for a year

From: Neurological and behavioral abnormalities, ventricular dilatation, altered cellular functions, inflammation, and neuronal injury in brains of mice due to common, persistent, parasitic infection

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]
  1. * Gene names and symbols from Entrez Gene [87] and function information from GeneCards [88]
  2. Either the number of genes in this category or the accession number
  3. 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.