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Table 1 Functional classification of differentially expressed genes at different time points of the disease (1, 60, 120 and 270 dpi) with a fold-change higher than 1.7 (up regulated genes) or lower than 0.6 (down regulated genes) at any of the four time points

From: Central nervous system gene expression changes in a transgenic mouse model for bovine spongiform encephalopathy

    Fold changes and p-values  
Functional group Gene symbol Gene description 1 dpi 60 dpi 120 dpi 270 dpi p -value Previous prion gene expression studies on the Central Nervous System
Immune, inflammatory and stress response Cxcl13 chemokine (C-X-C motif) ligand 13 1.59 0.91 0.90 30.48 < 1.00E-04 [18] (S), [37] (S), [38] (S)
  Clec7a C-type lectin domain family 7, member a 1.00 1.02 0.90 3.56 < 1.00E-04 [18] (S), [32] (S), [37] (S)
  Cybb cytochrome b-245, beta polypeptide 1.14 1.33 0.84 2.87 < 1.00E-04 [37] (S)
  C4 complement component 4 (within H-2S) 0.95 1.17 0.88 2.77 < 1.00E-04 [18] (S), [28] (S), [32] (S), [34] (S,CJD), [38] (S)
  Serpina3n serine (or cysteine) peptidase inhibitor, clade A, member 3N 0.82 0.85 0.56 2.50 < 1.00E-04 [18] (S), [32] (S), [34] (S,CJD), [37] (S), [36] (S)
  Rrm2b ribonucleotide reductase M2 B (TP53 inducible) 0.97 0.52 1.34 2.37 4.00E-04  
  C3 complement component 3 0.90 1.12 0.93 2.35 2.00E-04 [18] (S), [28] (S), [32] (S), [38] (S)
  C1qb complement component 1, q subcomponent, beta polypeptide 1.02 0.91 0.94 2.20 < 1.00E-04 [27] (S), [18] (S), [28] (S), [19] (S), [9] (S), [12] (S), [32, 34] (S/CJD)
  C1qa complement component 1, q subcomponent, alpha polypeptide 1.04 1.01 0.98 2.14 < 1.00E-04 [18] (S), [28] (S), [19] (S), [12] (S), [32, 34] (S/CJD)
  C1qg complement component 1, q subcomponent, gamma polypeptide 1.07 0.88 0.88 2.14 < 1.00E-04 [18] (S), [32] (S)
  Osmr oncostatin M receptor 0.82 1.08 0.97 2.13 < 1.00E-04 [18] (S), [28] (S), [32] (S), [37] (S)
  C3ar1 complement component 3a receptor 1 0.72 1.02 0.99 2.03 < 1.00E-04 [18] (S), [28] (S), [32] (S)
  Cd14 CD14 antigen 0.88 0.96 0.95 1.93 < 1.00E-04 [18] (S), [32] (S), [37] (S), [38] (S)
  Mpeg1 macrophage expressed gene 1 0.87 1.09 0.94 1.90 1.00E-04 [18] (S), [34] (S/CJD), [37] (S)
  Lilrb4 leukocyte immunoglobulin-like receptor, subfamily B, member 4 0.67 0.92 1.10 1.90 5.00E-04  
  Ly86 lymphocyte antigen 86 1.11 0.94 0.88 1.88 < 1.00E-04 [18] (S), [8] (S), [34] (S/CJD), [35] (S), [37] (S)
  Tlr2 toll-like receptor 2 0.97 1.12 0.93 1.84 < 1.00E-04 [18] (S), [32] (S), [34] (S/CJD), [37] (S)
  Hspb6 heat shock protein, alpha-crystallin-related, B6 0.98 1.03 1.10 1.82 < 1.00E-04  
  Cd48 CD48 antigen 0.82 0.89 0.88 1.81 < 1.00E-04 [18] (S)
  Icsbp1 interferon consensus sequence binding protein 1 0.91 1.02 0.95 1.76 < 1.00E-04 [18] (S), [28] (S)
  Ifi27 interferon, alpha-inducible protein 27 0.97 0.96 0.89 1.75 6.00E-04  
  Usp18 ubiquitin specific peptidase 18 0.87 1.04 0.80 1.72 3.00E-04 [37] (S)
  Socs3 suppressor of cytokine signaling 3 0.78 0.86 0.90 1.72 7.00E-04 [18] (S)
  Dusp1 dual specificity phosphatase 1 1.38 0.65 0.73 0.50 1.00E-04 [38] (S)
  Map4k2 mitogen activated protein kinase kinase kinase kinase 2 0.98 1.25 0.90 0.44 1.00E-04  
  Mamdc1 (Mdga2 VALIDATED)) MAM domain containing 1 (MAM domain containing glycosylphosphatidylinositol anchor 2 (VALIDATED)) 0.44 2.21 0.40 0.25 0.001  
Glial response Gfap glial fibrillary acidic protein 0.89 1.06 0.99 3.37 < 1.00E-04 [85] (S), [86] (S/AD) [18] (S), [19] (S), [28] (S), [30] (CJD), [12] (S), [31] (S), [34] (S/CJD), [35] (S), [37] (S)
  Cst7 cystatin F (leukocystatin) 0.99 1.08 0.97 3.24 < 1.00E-04 [18] (S), [28] (S), [32] (S), [37] (S)
  Lgals3 lectin, galactose binding, soluble 3 0.57 1.10 0.78 2.65 < 1.00E-04 [18] (S), [28] (S), [37] (S)
  Cd68 CD68 antigen 0.80 0.99 0.82 2.04 < 1.00E-04 [18] (S), [28] (S), [32] (S), [37] (S), [38] (S)
  Tyrobp TYRO protein tyrosine kinase binding protein 1.02 1.04 0.84 1.99 < 1.00E-04 [18] (S), [9] (S), [34] (S/CJD), [37] (S), [38] (S)
  Mt2 metallothionein 2 0.84 1.14 1.43 1.86 < 1.00E-04 [27] (S), [30] (CJD), [10] (BSE), [38] (S)
Cell death Rrm2b ribonucleotide reductase M2 B (TP53 inducible) 0.97 0.52 1.34 2.37 4.00E-04  
  Ctsc cathepsin C 0.96 0.81 1.05 1.81 < 1.00E-04 [18] (S), [28] (S), [37] (S), [36] (S)
  Bcl2a1a B-cell leukemia/lymphoma 2 related protein A1a 1.01 0.97 1.01 1.70 6.00E-04 [18] (S), [32] (S)
  1110006I15Rik (tmem109 (PROVISIONAL)) RIKEN cDNA 1110006I15 gene (transmembrane protein 109 (PROVISIONAL)) 0.80 1.29 1.40 0.56 5.00E-04  
  AA536749 (mprip VALIDATED)) expressed sequence AA536749 (myosin phosphatase Rho interacting protein (VALIDATED)) 0.85 1.45 1.02 0.53 3.00E-04  
  Nr4a1 nuclear receptor subfamily 4, group A, member 1 1.53 0.65 0.68 0.49 < 1.00E-04 [9] (S), [38] (S)
Cell adhesion Cd44 CD44 antigen 0.87 0.92 0.82 2.13 1.00E-04 [18] (S), [38] (S)
  Itgax integrin alpha X 0.95 1.06 0.89 1.79 < 1.00E-04 [18] (S), [37] (S)
  Gpnmb glycoprotein (transmembrane) nmb 0.71 1.08 1.01 1.74 9.00E-04 [18] (S), [37] (S)
  Ptprd protein tyrosine phosphatase, receptor type, D 0.93 2.67 0.75 0.39 1.00E-04  
Intracellular transport Snx6 sorting nexin 6 1.61 0.69 1.32 2.24 4.00E-04  
  Ndel1 nuclear distribution gene E-like homolog 1 (A. nidulans) 1.06 0.56 0.96 2.11 1.00E-04  
  Snx14 sorting nexin 14 0.83 0.78 1.16 1.84 < 1.00E-04  
  Vps37c vacuolar protein sorting 37C (yeast) 0.82 1.03 1.21 0.55 < 1.00E-04  
  Scfd1 sec1 family domain containing 1 0.62 1.51 0.67 0.52 4.00E-04  
  Rtn3 reticulon 3 0.85 1.66 0.96 0.34 < 1.00E-04 [9] (S), [15] (BSE)
Transmission of nerve impulse Tyrobp TYRO protein tyrosine kinase binding protein 1.02 1.04 0.84 1.99 < 1.00E-04 [18] (S), [9] (S), [34] (S/CJD), [37] (S), [38] (S)
  Slc6a4 solute carrier family 6 (neurotransmitter transporter, serotonin), member 4 1.12 1.62 0.99 0.60 0.0012  
  Arc activity regulated cytoskeletal-associated protein 2.20 0.66 0.96 0.45 < 1.00E-04  
  Pmch pro-melanin-concentrating hormone 0.98 1.27 0.83 0.44 < 1.00E-04  
  Egr2 early growth response 2 1.58 0.49 0.56 0.36 1.00E-04  
  Scn2b sodium channel, voltage-gated, type II, beta 0.96 1.57 0.97 0.09 < 1.00E-04  
Signal transduction S100a6 S100 calcium binding protein A6 (calcyclin) 0.92 0.93 0.89 1.93 < 1.00E-04 [18] (S), [29] (S)
  Hpgd hydroxyprostaglandin dehydrogenase 15 (NAD) 0.86 0.98 0.95 1.93 < 1.00E-04 [37] (S)
  Adamts4 a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 4 0.55 1.25 0.81 0.60 4.00E-04  
  Nr4a1 nuclear receptor subfamily 4, group A, member 1 1.53 0.65 0.68 0.49 < 1.00E-04 [9] (S), [38] (S)
  Ptprd protein tyrosine phosphatase, receptor type, D 0.93 2.67 0.75 0.39 1.00E-04  
Transcription Npas3 neuronal PAS domain protein 3 1.80 0.57 1.64 2.42 4.00E-04  
  Tle4 transducin-like enhancer of split 4, homolog of Drosophila E(spl) 0.97 0.91 0.79 1.99 < 1.00E-04  
  Cbx7 chromobox homolog 7 0.93 0.87 1.19 1.96 4.00E-04  
  Smad4 MAD homolog 4 (Drosophila) 0.67 0.73 2.02 1.33 2.00E-04  
  Klf2 Kruppel-like factor 2 (lung) 1.28 0.82 0.78 0.57 1.00E-04  
  Tle1 transducin-like enhancer of split 1, homolog of Drosophila E(spl) 0.87 1.88 0.77 0.56 0.0012  
  Junb Jun-B oncogene 1.41 0.51 0.65 0.53 < 1.00E-04 [9] (S)
  Cnot4 CCR4-NOT transcription complex, subunit 4 0.71 1.39 0.66 0.46 4.00E-04  
  Fos FBJ osteosarcoma oncogene 1.47 0.57 0.54 0.39 1.00E-04 [10] (BSE), [38] (S)
  Mysm1 myb-like, SWIRM and MPN domains 1 1.48 2.42 0.84 0.33 < 1.00E-04  
Biosynthetic process Rrm2b ribonucleotide reductase M2 B (TP53 inducible) 0.97 0.52 1.34 2.37 4.00E-04  
  Rpl17 ribosomal protein L17 1.32 1.38 0.34 0.66 4.00E-04  
  Pbx1 pre B-cell leukemia transcription factor 1 0.46 1.51 0.79 0.54 < 1.00E-04  
  2310043N10Rik (Neat1 (PROVISIONAL)) RIKEN cDNA 2310043N10 gene (nuclear paraspeckle assembly transcript 1 (non-protein coding) (PROVISIONAL)) 0.90 1.64 0.71 0.38 < 1.00E-04  
  4933439C20Rik (pisd-ps3 PROVISIONAL) RIKEN cDNA 4933439C20 gene (phosphatidylserine decarboxylase, pseudogene 3 (PROVISIONAL) 0.79 2.67 0.99 0.14 5.00E-04  
Others MGI:1929709 plasma membrane associated protein, S3-12 0.87 1.54 1.98 2.73 < 1.00E-04 [18] (S)
  1700047I17Rik (fam177a (PREDICTED)) RIKEN cDNA 1700047I17 gene (family with sequence similarity 177, member A (PREDICTED)) 1.77 0.52 1.81 2.57 1.00E-04  
  Cd52 CD52 antigen 1.16 0.91 0.88 2.54 < 1.00E-04 [18] (S), [28] (S), [34] (S/CJD), [37] (S)
  4930511A21Rik (ppp2r3c (VALIDATED)) RIKEN cDNA 4930511A21 gene (protein phosphatase 2, regulatory subunit B'', gamma (VALIDATED)) 1.36 0.64 1.33 1.83 7.00E-04  
  AU020206 expressed sequence AU020206 1.01 0.94 0.99 1.83 3.00E-04 [18] (S)
  A2m alpha-2-macroglobulin 0.88 0.91 1.02 1.76 1.00E-04 [18] (S), [28] (S), [37] (S), [38] (S)
  Ifi44 interferon-induced protein 44 0.82 0.97 0.87 1.74 0.0011  
  AI467657 (Zbtb16 (PROVISIONAL) expressed sequence AI467657 (zinc finger and BTB domain containing 16 (PROVISIONAL)) 0.76 1.53 2.09 1.61 < 1.00E-04  
  Mapk4 mitogen-activated protein kinase 4 0.87 0.93 1.81 1.32 < 1.00E-04  
  Atxn7l4 ataxin 7-like 4 0.55 1.24 0.87 0.74 8.00E-04  
  Cdca1 cell division cycle associated 1 0.59 1.25 0.89 0.61 < 1.00E-04  
  1700063D05Rik RIKEN cDNA 1700063D05 gene 1.01 0.90 0.95 0.60 < 1.00E-04  
  2700081O15Rik RIKEN cDNA 2700081O15 gene 0.98 1.13 0.98 0.59 < 1.00E-04  
  Btg2 B-cell translocation gene 2, anti-proliferative 1.20 0.83 0.86 0.58 2.00E-04 [38] (S)
  Lrfn5 leucine rich repeat and fibronectin type III domain containing 5 0.54 1.67 0.81 0.57 5.00E-04 [33] (S)
  Gm1075 gene model 1075, (NCBI) 1.31 0.74 0.56 0.56 < 1.00E-04  
  Prp19 PRP19/PSO4 homolog (S. cerevisiae) 0.95 1.42 1.25 0.48 < 1.00E-04 [10] (BSE)
  R75368 (palm2 (VALIDATED)) expressed sequence R75368 (paralemmin 2 (VALIDATED)) 1.06 2.49 0.62 0.47 5.00E-04  
  1. Assignation of the gene function was made according to the Babelomics 3.2 tool [24] and subsequently manually curated. (S = scrapie, BSE = Bovine Spongiform Encephalopathy, CJD = Creutzfeldt-Jakob disease).