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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).