Table 3. Differentially expressed genes identified by previous studies of prion infected animals.

Gene Name	Previous studies	Organism	Tissue	Prion
Actin, gamma 2, smooth muscle, enteric	Booth et al. 2004; Skinner et al. 2006 ; Sorensen et al., 2008 Sawiris et al., 2007	Mice Mice	Brain Brain	Scrapie BSE
ADAM-like, decysin 1	Sorensen et al., 2008	Mice	Brain	Scrapie
Amyloid β (A4) precursor protein	Sorensen et al., 2008 Sawiris et al., 2007	Mice Mice	Brain Brain	Scrapie BSE
ATP synthase, H+ transporting, mitochondrial	Sawiris et al., 2007	Mice	Brain	BSE
ATPase, Na+/K+ transporting	Booth et al. 2004; Skinner et al. 2006 ; Sorensen et al., 2008 Sawiris et al., 2007	Mice Mice	Brain Brain	Scrapie BSE
Calponin 1	Almeida et al., 2011	Cow	Medulla	BSE
Carbonic anhydrase II	Skinner et al., 2006	Mice	Brain	Scrapie
Cadherin E	Khanyia et al., 2009 Almeida et al., 2011	Cow Cow	Peyer’s Patch Medulla	BSE BSE
Cathepsin H	Xiang et al., 2004; Riemer et al., 2004; Sorensen et al., 2008	Mice	Brain	Scrapie
Chemokine (C-C motif) ligand 2, 20, 21,	Xiang et al., 2004; Sawiris et al., 2007	Mice	Brain	Scrapie
Citrate synthase	Sawiris et al., 2007	Mice	Brain	BSE
Cocaine and amphetamine responsive transcript	Sorensen et al., 2008; Almeida et al., 2011	Mice Cow	Brain Medulla	Scrapie BSE
Creatine kinase, mitochondrial 1	Greenwood et al., 2005	Mice	Neuroblastoma cells	Scrapie
Desmin	Almeida et al., 2011	Cow	Medulla	BSE
DnaJ (Hsp40) homolog, subfamily A, member 1	Sorensen et al., 2008	Mice	Brain	Scrapie
ELMO/CED-12 domain containing 1	Almeida et al., 2011	Cow	Medulla	BSE
Filamin A, α	Sorensen et al., 2008 Almeida et al., 2011	Mice Cow	Brain Medulla	Scrapie BSE
Fibulin 5	Sawiris et al., 2007	Mice	Brain	BSE
FK506 binding protein 1B, 12.6 kDa	Sorensen et al., 2008	Mice	Brain	Scrapie
Growth associated protein 43	Greenwood et al., 2005	Mice	Neuroblastoma cells	Scrapie
Guanine nucleotide binding protein	Sorensen et al., 2008	Mice	Brain	Scrapie
Heat shock 70kDa protein	Sorensen et al., 2008	Mice	Brain	Scrapie
Interleukin 8	Booth et al., 2004; Skinner et al., 2006; Sorensen et al., 2008	Mice Mice	Brain Brain	Scrapie BSE
Kinesin-associated protein 3	Skinner et al., 2006; Sawiris et al., 2007	Mice Mice	Brain Brain	Scrapie BSE
Leucine rich repeat transmembrane neuronal 1	Sorensen et al., 2008	Mice	Brain	Scrapie
Lymphocyte antigen 75	Skinner et al., 2006 ; Sorensen et al., 2008	Mice	Brain	Scrapie
Lymphocyte cytosolic protein 1	Xiang et al., 2004	Mice	Brain	Scrapie
Lysozyme 1	Riemer et al., 2004	Mice	Brain	Scrapie
Macrophage scavenger receptor 1	Xiang et al., 2004	Mice	Brain	Scrapie
Major histocompatibility complex, class II	Riemer et al., 2004 Basu et al., 2011	Mice Cow	Brain Medulla	Scrapie BSE
Matrix metallopeptidase 7	Sorensen et al., 2008	Mice	Brain	Scrapie
MHC class I heavy chain	Riemer et al., 2004	Mice	Brain	Scrapie
Malate dehydrogenase 1, NAD	Sawiris et al., 2007 Skinner et al., 2006	Mice Mice	Brain Brain	BSE Scrapie
Membrane-spanning 4-domains	Sawiris et al., 2007	Mice	Brain	BSE
Metallothionein 1E	Greenwood et al., 2005	Mice	Neuroblastoma cells	Scrapie
Mitogen-activated protein kinase 10	Riemer et al.,2004	Mice	Brain	Scrapie
Multiple coagulation factor deficiency 2	Martínez and Pascual, 2007	Human	Neuroblastoma cells	Peptide 106–126
Myosin, heavy chain 10, non-muscle	Martínez and Pascual, 2007	Human	Neuroblastoma cells	Peptide 106–126
Myosin, light chain 1; Myosin, light chain 9	Sorensen et al., 2008	Mice	Brain	Scrapie
Neurofilament, medium polypeptide	Skinner et al., 2006; Sorensen et al., 2008	Mice	Brain	Scrapie
Neurotrophic tyrosine kinase, receptor	Skinner et al., 2006	Mice	Brain	Scrapie
Neuropeptide Y	Diez et al., 2007	Mice	Brain	RML or ME7
PDZ and LIM domain 3	Sawiris et al., 2007	Mice	Brain	BSE
P21 (CDKN1A)-activated kinase 3	Sawiris et al., 2007	Mice	Brain	BSE
Parvalbumin	Voigtländer et al., 2008 Almeida et al., 2011	Mice Cow	Brain Medulla	Scrapie BSE
Phosphoglycerate mutase 1 (brain)	Sawiris et al., 2007	Mice	Brain	BSE
Pleiotrophin	Sorensen et al., 2008	Mice	Brain	Scrapie
Potassium voltage-gated channel	Sawiris et al., 2007	Mice	Brain	BSE
Potassium channel tetramerisation domain containing 15	Sorensen et al., 2008 Sawiris et al., 2007	Mice Mice	Brain Brain	Scrapie BSE
Potassium inwardly-rectifying channel	Skinner et al., 2006	Mice	Brain	Scrapie
Proliferating cell nuclear antigen	Sorensen et al., 2008	Mice	Brain	Scrapie
Protein S (α)	Xiang et al., 2004	Mice	Brain	Scrapie
Protein tyrosine phosphatase	Xiang et al., 2004; Sorensen et al., 2008 Martínez and Pascual, 2007	Mice Human	Brain Neuroblastoma cells	Scrapie Peptide 106–126
Ras homolog gene family	Sorensen et al., 2008	Mice	Brain	Scrapie
Regulator of chromosome condensation (RCC1)	Sorensen et al., 2008	Mice	Brain	Scrapie
Ribosomal protein S6 kinase, 70kDa	Martínez and Pascual, 2007	Human	Neuroblastoma cells	Peptide 106–126
Ribosomal protein S15	Sorensen et al., 2008 Sawiris et al., 2007 Greenwood et al., 2005	Mice Mice Mice	Brain Brain Neuroblastoma cells	Scrapie BSE Scrapie
S100 calcium binding protein A9	Xiang et al., 2004	Mice	Brain	Scrapie
Sarcoglycan, β	Sorensen et al., 2008	Mice	Brain	Scrapie
Secretogranin II	Skinner et al., 2006 Greenwood et al., 2005	Mice Mice	Brain Neuroblastoma cells	Scrapie Scrapie
Septin 7	Booth et al., 2004; Skinner et al., 2004; Sorensen et al., 2008	Mice	Brain	Scrapie
Solute carrier family 39	Martínez and Pascual, 2007	Human	Neuroblastoma cells	Peptide 106–126
SPARC-like 1	Skinner et al., 2006	Mice	Brain	Scapie
Spastic paraplegia 3A	Sorensen et al., 2008	Mice	Brain	Scrapie
Stathmin-like 2	Greenwood et al., 2005	Mice	Neuroblastoma cells	Scrapie
Stearoyl-CoA desaturase	Booth et al., 2004; Sorensen et al., 2008	Mice	Brain	Scrapie
Succinate-CoA ligase, ADP-forming	Martínez and Pascual, 2007	Human	Neuroblastoma cells	Peptide 106–126
Superoxide dismutase 1	Greenwood et al., 2005 Larska et al.,2010	Mice Cattle	Neuroblastoma cells Brain	Scrapie BSE
Synaptosomal-associated protein, 25kDa	Booth et al., 2004; Skinner et al., 2004; Sorensen et al., 2008 Basu et al., 2011; Almeida et al., 2011	Mice Cow	Brain Medulla	Scrapie BSE
Syndecan	Sorensen et al., 2008	Mice	Brain	Scrapie
Thy-1 cell surface antigen	Sorensen et al., 2008	Mice	Brain	Scrapie
Tachykinin, precursor 1	Almeida et al., 2011	Cow	Medulla	BSE
Transgelin	Sawiris et al., 2007	Mice	Brain	BSE
Transthyretin (prealbumin, amyloidosis)	Sorensen et al., 2008	Mice	Brain	Scrapie
Tropomyosin 2 (β)	Martínez and Pascual, 2007 Almeida et al., 2011	Human Cow	Neuroblastoma cells Medulla	Peptide 106–126 BSE
Tubulin, β 2B	Sorensen et al., 2008	Mice	Brain	Scrapie

Genes identified in elk brain, midbrain and thalamus (black letter) and in elk spleen, RPLN and tonsil tissues (gray letter).