Table 2. Gene Ontology (GO) analysis of differentially expressed genes with ≥ 2.0 fold change, associated with CWD disease in spleen (SP), retropharyngeal lymph nodes (RPLN) and tonsil (TO) tissues of elk.

GO Function (Biological and Molecular processes)	Gene ID	Gene Name	SP	RPLN	TO
Apoptosis and cell cycle	Bt.64777 Bt.64827 Bt.2408 Bt.13573 Bt.15980	Baculoviral IAP repeat-containing 3 Cadherin 1, E-cadherin (epithelial) Chemokine (C-C motif) ligand 2 CDC28 protein kinase regulatory subunit 2 Cyclin B1	2.03 2.72 2.10 2.38		-2.02
	Bt.4539 Bt.34390 Bt.4922 Bt.6324 Bt.357 Bt.76113 Bt.87249	Angiotensin II receptor, type 1 Cysteine and glycine-rich protein Myosin, light chain 1, alkali Myosin, light chain 9, regulatory S100 calcium binding protein A12 (calgranulin C) S100 calcium binding protein A14 S100 calcium binding protein A9	-2.34 2.46 2.11 -3.79 2.69		-4.86 -2.12 -5.63
Calcium binding and regulation	Bt.66812 Bt.59155 Bt.15705 Bt.97 Bt.4057 Bt.120	Sarcoglycan, β Cytokeratin 19 Destrin (actin depolymerizing factor) Fatty acid binding protein 4, adipocyte Myosin, heavy chain 10, non-muscle Rho-associated, coiled-coil containing protein kinase 2	-2.28 2.21 -3.47 -5.11 -2.15 -2.67
Cytoskeleton organization and cytokinesis	Bt.59726 Bt.16055 Bt.9714 Bt.575 Bt.6141 Bt.45294 Bt.89332 Bt.45158 Bt.62630 Bt.4703 Bt.33253 Bt.64757 Bt.8880 Bt.49324 Bt.74664 Bt.53077 Bt.97350 Bt.8897 Bt.41406	Caldesmon 1 Transgelin Actin, gamma 2, smooth muscle, enteric Common salivary protein BSP30 form a Desmin Elongation factor RNA polymerase II Fibroblast growth factor-binding protein Filamin A, α Mal, T-cell differentiation protein 2 Myocilin Myotilin Neurotrophic tyrosine kinase, receptor SPARC-like 1 (mast9, hevin) Stress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein) Tensin 3 Tropomyosin 2 (β) Troponin C type 2 (fast) Von Ebner minor salivary gland protein Zinc finger protein 618	-5.00 -3.00 -3.81 -3.91 2.02 -2.17 2.77 2.50 -2.25 -3.45 2.53 -2.84 -3.37 2.02 2.75		-5.83 -2.57 -2.76
Immune and inflammatory response	Bt.91780 Bt.4259 Bt.88495 Bt.9560 Bt.26536 Bt.13542 Bt.68530 Bt.49740 Bt.89770 Bt.29871 Bt.62645 Bt.88760	Cathelicidin 1 Cathelicidin 2 Cathelicidin 6 Chemokine (C-C motif) ligand 20 Chemokine (C-C motif) ligand 21 Complement factor B Complement factor H Interleukin 8 Lysozyme (renal amyloidosis) Major histocompatibility complex, class II, DY α MHC class I heavy chain Serum amyloid A-like	-6.61 -9.89 -2.98 3.29 2.51 -2.78 3.82 2.05 4.51	-2.09	2.70 -3.03
Protein folding	Bt.88837 Bt.21932	DnaJ (Hsp40) homolog, subfamily A, member 1 F-box protein 7	2.53 2.24	2.14
Proteolysis	Bt.77495 Bt.12553 Bt.13092	ADAM-like, decysin 1 Haptoglobin Matrix metallopeptidase 7	3.07 4.78	3.32
Regulation of transcription	Bt.22888 Bt.87332 Bt.45673	Nuclear receptor subfamily 3, group C Similar to HMGB2 protein Spi-C transcription factor	-3.05 2.38 -7.14
Signal transduction	Bt.44951 Bt.53744 Bt.3081 Bt.21143 Bt.20059 Bt.3704 Bt.6915 Bt.9632 Bt.61075	Intersectin 1 (SH3 domain protein) IQ motif containing GTPase activating protein 1 Membrane-spanning 4-domains Rho GTPase activating protein 29 Ribosomal protein S6 kinase, 70kDa Stathmin-like 2 CD163 molecule Deleted in malignant brain tumors 1 Similar to macrophage receptor MARCO	-2.19 -2.38 -2.57 -5.46 -2.36 -2.28	-2.01	2.48 2.01
Transport	Bt.49731 Bt.79147 Bt.10591 Bt.45049 Bt.4482 Bt.43781 Bt.14388 Bt.47454 Bt.52764 Bt.22651	Carbonic anhydrase II Growth hormone receptor Hemoglobin α chain Hemoglobin, β Macrophage scavenger receptor 1 NECAP endocytosis associated 2 Potassium channel tetramerisation domain containing 15 Potassium voltage-gated channel Proliferating cell nuclear antigen Solute carrier family 39 (zinc transporter)	-2.22 -2.14 -7.54 -19.6 -3.81 -3.51 2.05 -2.00	2.11	-2.69
Cellular process	Bt.48705 Bt.37052 Bt.28966 Bt.67194 Bt.30108 Bt.37111 Bt.57571 Bt.4844 Bt.42764 Bt.61915 Bt.20277 Bt.58848 Bt.49598	GINS complex subunit 4 Hemicentin 1 Hypothetical protein LOC100125947 Lysozyme 1 Meiotic nuclear divisions 1 homolog Microtubule-associated protein 1B PDZ and LIM domain 3 Pleiotrophin Prosaposin Similar to 90-kDa heat shock protein α Topoisomerase (DNA) II α 170kDa Ubiquitin carboxyl-terminal esterase L1 Cysteine-rich, angiogenic inducer, 61	2.02 -2.90 4.22 2.68 2.18 -2.55 -2.15 -3.45 -2.14 2.12 2.22 -2.15	2.28 2.49
Cell adhesion	Bt.63411 Bt.44183 Bt.9807 Bt.20373 Bt.121	Cadherin 18, type 2 Fibulin 5 Glycoprotein (transmembrane) nmb Neuropilin 1 Frizzled-related protein	-2.03 -2.69 -2.92 -2.08 -2.21
Structure Organization	Bt.6630 Bt.13391	Calponin 1, basic, smooth muscle Capping protein (actin filament) muscle Z-line, α 2	-4.60		-2.03
Response to stimulus	Bt.4001 Bt.51574 Bt.8738 Bt.12309 Bt.96882	Heme oxygenase (decycling) 1 Caveolin 1, caveolae protein, 22kDa Heat shock 105kDa/110kDa protein 1 Heat shock 70kDa protein 8 Similar to RIKEN cDNA 1110064P04 gene	-3.81 -2.02 2.10 2.44	3.14
Angiogenese and axonogenesis	Bt.91353 Bt.5240 Bt.40062 Bt.3137	Angiopoietin 1 Connective tissue growth factor Amyloid β (A4) precursor protein (peptidase nexin-II, Alzheimer disease) Stathmin 1/oncoprotein 18	-2.52 -2.12 2.62	2.10
Phosphatase activity	Bt.20846	CTD (C-terminal domain, RNA polymerase II, polypeptide A)	-2.00