Table 2.

GO terms for differentially expressed genes

Term	P value	ProbeName	FC (C vs NC)	FC (PC vs NC)	Gene symbol	Gene name	Citation
Glycoprotein	5.16E-04	A_70_P042906	2.22	1.00	AQP1	Aquaporin 1 (Colton blood group)
		CUST_5666_PI375351158	−2.02	−1.16	AQP4	Aquaporin 4	[10]
		A_70_P041077	2.09	1.39	PTGER3	Prostaglandin E receptor 3 (subtype EP3)
		A_70_P030356	1.48	−2.06	SLC11A1	Solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1
		A_70_P051037	−2.09	2.85	SLC2A5	Solute carrier family 2 (facilitated glucose/fructose transporter), member 5	[10]
		A_70_P036386	−1.29	−2.01	UCHL1*	Ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase)
Extracellular region	5.37E-04	CUST_2502_PI375351158	2.26	2.76	BMPER	BMP binding endothelial regulator
		A_70_P006426	4.26	1.06	FGL1	Fibrinogen-like 1
		A_70_P069571	2.05	1.93	FIBIN	Fin bud initiation factor homolog (zebrafish)
		A_70_P038041	1.95	−3.63	HP	Haptoglobin	[10]
		CUST_3439_PI375351158	2.70	1.38	PIGR	Polymeric immunoglobulin receptor
		A_70_P035871	1.03	−3.29	SERPINE1*	Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1
		A_70_P039451	−1.57	−2.28	SFN	Stratifin
		A_70_P050922	2.19	−1.06	VEGFA*	Vascular endothelial growth factor A
Disulfide bond	1.10E-03	CUST_598_PI375351158	2.28	1.33	FABP5	Fatty acid binding protein 5 (psoriasis-associated)
		A_70_P070736	−3.83	−1.06	TXNRD1	Thioredoxin reductase 1
Cell cycle	1.17E-03	A_70_P058586	−2.85	−1.55	PSMA7*	Proteasome (prosome, macropain) subunit, alpha type, 7
		A_70_P057841	−1.61	−2.51	BRCA2	Breast cancer 2, early onset
		A_70_P053686	1.11	−2.01	CCNDBP1	Cyclin D-type binding-protein 1
		A_70_P060136	−1.48	−2.04	CGREF1	Cell growth regulator with EF-hand domain 1
		A_70_P027076	−2.79	−1.28	EID1	EP300 interacting inhibitor of differentiation 1
		A_70_P007666	−2.87	−1.61	KIF2C	Kinesin family member 2C
		A_70_P011891	−2.34	−1.29	MND1	Meiotic nuclear divisions 1 homolog (S. cerevisiae)
		A_70_P009551	−2.13	−1.07	NCAPG	Non-SMC condensin I complex, subunit G
		A_70_P037556	−2.12	1.01	NDC80	NDC80 homolog, kinetochore complex component (S. cerevisiae)
		A_70_P034256	−2.20	1.05	TFDP2	Transcription factor Dp-2 (E2F dimerization partner 2)
		A_70_P061801	−2.01	−1.39	UBE2C	Ubiquitin-conjugating enzyme E2C
Condensed chromosome	1.71E-03	CUST_7895_PI375351158	−2.79	−1.15	HMGB1	High-mobility group box 1
		A_70_P003816	−2.20	−1.67	TEX12	Testis expressed 12
Alternative splicing	2.04E-03	A_70_P059171	−2.57	−2.17	CLTA	Clathrin, light chain (Lca)
		A_70_P033441	1.13	2.27	MEST	Mesoderm specific transcript homolog (mouse)
		A_70_P039536	−2.86	−1.34	MX1	Myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)
		A_70_P060791	2.25	1.38	PEG3	Paternally expressed 3
		A_70_P015446	−1.52	−2.13	UNC50	Unc-50 homolog (C. elegans)
Chromosome	2.20E-03	A_70_P065046	−2.68	−1.32	JRKL	Jerky homolog-like (mouse)
		A_70_P040916	−2.62	−1.67	ORC1L	Origin recognition complex, subunit 1-like (yeast)
		CUST_12205_PI375351158	−2.04	−1.20	TOP2A	Topoisomerase (DNA) II alpha 170 kDa	[33]
Extracellular matrix	3.15E-03	A_70_P021711	−2.19	−1.69	COL1A1	Collagen, type I, alpha 1	[10,16]
		CUST_11292_PI375351158	2.40	1.12	CRISPLD2	Cysteine-rich secretory protein LCCL domain containing 2
		A_70_P007356	2.20	1.26	DCN	Decorin	[10,16]
		CUST_7449_PI375351158	1.46	−2.05	DPT	Dermatopontin
		A_70_P032476	2.45	−1.35	MFAP5	Microfibrillar associated protein 5	[10]
		A_70_P058626	2.27	1.13	VWF	Von Willebrand factor
Signal peptide	3.25E-03	A_70_P064081	2.44	−2.18	CA4	Carbonic anhydrase IV
		A_70_P061221	1.20	−2.43	P4HA1	Prolyl 4-hydroxylase, alpha polypeptide I	[10,11]
		A_70_P040831	−2.09	−1.07	SELL	Selectin L
Tumor suppressor	1.47E-02	A_70_P035971	2.05	−1.75	VWA5A	Von Willebrand factor A domain containing 5A
		A_70_P026737	3.11	−1.41	WT1	Wilms tumor 1
		A_70_P061691	1.26	2.26	HPGD	Hydroxyprostaglandin dehydrogenase 15-(NAD)
Cytoplasm	1.82E-02	A_70_P016337	−1.78	−2.72	HMMR	Hyaluronan-mediated motility receptor (RHAMM)
		CUST_12176_PI375351158	−1.04	−2.92	ACTG2	Actin, gamma 2, smooth muscle, enteric
		A_70_P019656	1.01	3.59	ADH1A	Alcohol dehydrogenase 1A (class I), alpha polypeptide
		A_70_P045301	3.70	2.33	BBOX1*	Butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1
		A_70_P069971	−2.09	−1.73	CDC42EP5	CDC42 effector protein (Rho GTPase binding) 5
		CUST_5823_PI375351158	1.12	2.07	NIN	Ninein (GSK3B interacting protein)
		A_70_P018021	−3.25	−1.15	PAIP2	Poly(A) binding protein interacting protein 2
		A_70_P054126	−2.16	−1.11	PHAX	Phosphorylated adaptor for RNA export
		A_70_P044246	1.26	−2.14	RRAGD	Ras-related GTP binding D
		A_70_P055106	2.05	1.07	SORBS2	Sorbin and SH3 domain containing 2
		A_70_P025726	−2.39	−1.60	STMN2	Stathmin-like 2
		A_70_P060991	−2.80	1.21	CA3	Carbonic anhydrase III, muscle specific
Fatty acid metabolism	2.26E-02	CUST_8730_PI375351158	1.06	−2.05	ACSL4	Acyl-CoA synthetase long-chain family member 4
		A_70_P039986	−1.27	2.39	SLC27A2	Solute carrier family 27 (fatty acid transporter), member 2
Phosphatidic acid metabolic process	2.86E-02	A_70_P039726	−2.50	−1.10	AGPAT1	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)
		A_70_P025121	−3.34	−1.30	PLA2G2A	Phospholipase A2, group IIA (platelets, synovial fluid)
Protein dimerization activity	2.91E-02	CUST_206_PI396851701	2.04	−2.28	FOS	v-fos FBJ murine osteosarcoma viral oncogene homolog	[10,11,33]
		CUST_10535_PI375351158	−2.41	−2.41	NFE2L1	Nuclear factor (erythroid-derived 2)-like 1
Zinc finger, C2H2-type	3.09E-02	CUST_13307_PI375351158	−2.34	−1.26	ATMIN	ATM interactor
		A_70_P036056	−2.65	−1.71	KLF6	Kruppel-like factor 6
		A_70_P065371	−2.27	−1.13	ZCCHC6	Zinc finger, CCHC domain containing 6
		A_70_P014286	1.33	2.01	ZNF45	Zinc finger protein 45
Cytoplasmic membrane-bounded vesicle	3.21E-02	A_70_P062831	−3.71	−1.48	EHD3	EH-domain containing 3
		A_70_P044621	2.27	−1.04	MALL	Mal, T-cell differentiation protein-like
Metal ion transport	3.39E-02	A_70_P030126	−2.36	1.24	CP*	Ceruloplasmin (ferroxidase)	[10,16]
		CUST_12632_PI375351158	2.28	1.50	KCTD12	Potassium channel tetramerisation domain containing 12
		A_70_P027206	2.15	2.10	SLC30A1	Solute carrier family 30 (zinc transporter), member 1	[10,11]
		A_70_P050456	−2.65	−1.58	SLC38A10	Solute carrier family 38, member 10
Antimicrobial	5.05E-02	CUST_139_PI396851701	15.26	−1.74	CATHL1	Cathelicidin 1
		CUST_3993_PI375351158	5.96	−1.25	S100A8	S100 calcium binding protein A8	[10]
Apoptosis	5.45E-02	CUST_260_PI396851701	−2.04	−1.55	CARD6	Caspase recruitment domain family, member 6
		A_70_P022526	−2.29	−1.16	OPA1	Optic atrophy 1 (autosomal dominant)
		A_70_P049526	−1.12	−2.70	PERP	PERP, TP53 apoptosis effector
		A_70_P069836	−3.14	−1.31	RNF130	Ring finger protein 130
		A_70_P067091	−2.90	−1.55	UBE2Z	Ubiquitin-conjugating enzyme E2Z
Immunoglobulin-like fold	5.55E-02	A_70_P036361	2.06	2.09	CD1E	CD1e molecule
		CUST_9656_PI375351158	−2.03	1.11	FGFR2	Fibroblast growth factor receptor 2
		CUST_12141_PI375351158	2.64	−1.00	IGK	Ig kappa chain
		A_70_P016986	−2.23	1.16	TRD@	T cell receptor delta locus	[11]
Secreted	5.70E-02	A_70_P048761	1.34	−2.27	SPINK5	Serine peptidase inhibitor, Kazal type 5
		CUST_9580_PI375351158	1.13	−2.49	MMRN1	Multimerin 1
		CUST_10101_PI375351158	−1.07	−2.53	NPNT	Nephronectin
		A_70_P034356	2.88	1.19	SEMA3G	Sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G
		A_70_P063891	2.38	−1.22	PCOLCE2	Procollagen C-endopeptidase enhancer 2
GTP binding	7.49E-02	A_70_P019676	4.33	1.16	ACSM1	Acyl-CoA synthetase medium-chain family member 1	[10]
		A_70_P046951	−2.24	−1.02	ARL4C	ADP-ribosylation factor-like 4C
		A_70_P008796	−2.06	1.15	DOCK11	Dedicator of cytokinesis 11
		A_70_P000126	−3.63	−1.82	GBP4	Guanylate binding protein 4
Disulfide bond	7.58E-02	A_70_P018376	2.56	−1.08	FAP	Fibroblast activation protein, alpha
		A_70_P041321	−2.15	−2.57	IGHA2	Immunoglobulin heavy constant alpha 2 (A2m marker)
Structural molecule activity	8.04E-02	A_70_P028306	−2.03	−1.05	LMNB1	Lamin B1
		CUST_13373_PI375351158	−2.15	−1.29	LOC531679	Ribosomal protein 17-like; similar to 60S ribosomal Protein L17 (L23); similar to ribosomal protein L17; similar to Rpl17 protein; similar to mCG3798
		CUST_7057_PI375351158	−2.33	−1.07	LOC789587	Similar to Ribosomal_L22 domain containing protein RGD1359290
		A_70_P031441	−2.43	−1.79	VCL	Vinculin	[11]
Positive regulation of inflammatory response	9.48E-02	A_70_P058551	8.25	−1.12	FABP4	Fatty acid binding protein 4, adipocyte
		CUST_9779_PI375351158	−1.40	−2.38	IDO1	Indoleamine 2,3-dioxygenase 1
Other		CUST_13467_PI375351158	1.29	−2.14	FBP2	Fructose-1,6-bisphosphatase 2
		A_70_P055306	2.77	1.50	SLC43A1	Solute carrier family 43, member 1
		A_70_P049406	−1.99	−2.32	EIF5	Eukaryotic translation initiation factor 5	[11]
		A_70_P070931	−2.87	−1.18	NUDT19	Nudix (nucleoside diphosphate linked moiety X)-type motif 19
		A_70_P036101	1.22	−3.18	NOP10	NOP10 ribonucleoprotein homolog (yeast)	[11]
		A_70_P011091	−2.74	−2.01	PFDN2*	Prefoldin subunit 2
		A_70_P039656	17.20	−1.52	BAC5	5 kDa bactinecin precursor
		A_70_P061341	−1.03	−2.94	C11ORF10	Chromosome 11 open reading frame 10
		A_70_P061266	2.36	1.03	C5ORF43	Chromosome 5 open reading frame 43
		A_70_P051377	14.99	−1.48	CATHL1B	Procyclic dodecapeptide
		A_70_P015101	−2.70	−1.03	CCDC82	Coiled-coil domain containing 82
		A_70_P012541	−1.02	−2.36	CNN1	Calponin 1, basic, smooth muscle
		A_70_P002841	2.03	1.48	EPAS	Endothelial PAS domain protein 1
		A_70_P008841	−2.18	−1.23	EPSTI1	Epithelial stromal interaction 1 (breast)
		A_70_P060756	−2.12	1.08	FAM190B	KIAA1128
		A_70_P062951	2.05	1.12	FNDC3B	Fibronectin type III domain containing 3B	[33]
		A_70_P051181	2.76	1.28	HSD11K	NAD-dependent 11-beta-hydroxysteroid dehydrogenase
		CUST_46_PI396851701	−2.06	−2.15	IGHA	Immunoglobulin heavy constant alpha
		A_70_P024671	2.46	1.31	INHBB	Inhibin, beta B
		A_70_P033656	−2.34	−1.77	ISG12(A)	ISG12(a) protein-like
		A_70_P012537	−2.19	−3.58	LGALS15	Galectin 15
		CUST_3620_PI375351158	−1.58	−2.22	LGALS16	Beta-galactoside-binding lectin
		A_70_P020131	−1.10	−3.84	LGALS9C	Lectin, galactoside-binding, soluble, 9C
		CUST_6089_PI375351158	−2.02	−1.71	LOC100140018	Similar to cytochrome P450, family 2, subfamily J
		A_70_P016801	−2.20	−1.48	LOC443321	Lysozyme 2a precursor
		A_70_P026671	−1.91	−2.05	LOC524810	IgM
		A_70_P023026	3.09	1.74	LOC615697	Similar to cytochrome P450
		A_70_P039266	−2.03	−1.83	LOC654331	Pancreatitis-associated protein I	[10]
		A_70_P039271	−3.94	−7.40	MCP-4	Mast cell proteinase-4
		CUST_11558_PI375351158	2.00	2.23	MGC140754	Hypothetical LOC508613
		CUST_9725_PI375351158	−2.26	−3.77	PLAC8	Placenta-specific 8
		CUST_10114_PI375351158	2.56	1.15	RN18S1	18S ribosomal RNA
		A_70_P030132	−2.40	−1.71	RTP4	Receptor (chemosensory) transporter protein 4	[34]
		A_70_P030426	10.95	1.39	SC5	Cathelin-related prepropeptide

*Genes selected for validation by quantitative RT-PCR.

BLAST results for clones exhibiting significant alterations in gene expression (P ≤ 0.05 and ≥ 2-fold change) in preclinical and clinical stages of natural scrapie. The GO was determined using DAVID Bioinformatics Resources 6.7 (NIAID/NIH, USA), an on-line functional annotation tool. Only genes with a known GO are shown. (C, Clinical; FC, Fold change; NC, Negative control; PC, Preclinical). Previous studies describing altered expression of the differentially expressed genes reported here in the brain and lymphoid tissues of experimentally-infected sheep are cited.