Table 3.

List of genes from microarray with RS vs. EC results and used in validation¹,² (alphabetical by abbreviation).

Name	Abbrev	NCBI Gene ID	Fold Change	p Value	Function (Pathway or Unclassified)
Acetyl-coenzyme A acyltransferase 3	Acat 3	308100	1.61	0.000	Unclassified
Actinin alpha 1	Actn1	81634	1.98	0.000	Integrin
Actinin alpha 4	Actn4	63836	1.97	0.000	Integrin
Adrenomedullin	Adm	25026	5.32	0.000	Unclassified
Aldehyde oxidase 3	Aox3	493909	0.56	0.004	Adenine and hypoxanthine salvage
Adaptor protein complex AP-2	Ap2a2	81637	1.51	0.004	Huntington Disease
Amphiregulin	Areg	29183	25.64	0.000	EGF receptor signaling
ADP-ribosylation factor 2	Arf2	79119	1.51	0.006	Huntington Disease + Integrin
ADP-ribosylation factor 3	Arf3	140940	1.78	0.002	Huntington Disease + Integrin
Rho GTPase activating protein 27	Arhgap27	303583	1.45	0.002	PDGF signaling
Rho GTPase activating protein 8	Arhgap8	300115	2.15	0.002	Angiogenesis + PDGF signaling + VEGF signaling + Cytoskeleton regulation by RhoGTPase
Asparagine synthetase	Asns	25612	2.73	0.000	Asparagine and aspartate biosynthesis
Activating transcription factor 3	Atf3	25389	3.26	0.000	Apoptosis
Beta-site APP-cleaving enzyme 2	Bace2	288227	0.5	0.004	Alzheimer disease-amyloid secretase
Bone morphogenetic protein 2	Bmp2	29373	1.31	0.009	TGF beta signaling
Bone morphogenetic protein 3	Bmp3	25667	2.48	0.030	Unclassified
Calcium channel, voltage-dependent, T type, alpha 1H subunit	Cacna1h	114862	3.12	0.005	Unclassified
Caspase 4	Casp4	114555	1.59	0.000	Unclassified
Cystathionine beta synthase	Cbs	24250	1.52	0.008	Cysteine biosynthesis
CD14 antigen	Cd14	60350	0.56	0.005	Toll-like receptor
Cyclin-dependent kinase	Cdk2	362817	1.59	0.006	p53 + p53 feedback loops 2
Cyclin-dependent kinase inhibitor 1A	Cdkn1a	114851	2.18	0.000	Interleukin + p53 feedback loops 2 + p53
Chromogranin A	Chga	24258	0.52	0.000	Unclassified
Chromogranin B	Chgb	24259	0.54	0.000	Unclassified
Collagen, type 5, alpha 3	Col5a3	60379	2.72	0.003	Integrin
Dual specificity phosphatase 1	Dusp1	114856	5.99	0.000	Unclassified
Dual specificity phosphatase 4	Dusp4	60587	2.96	0.000	Oxidative stress response
Dual specificity phosphatase 5	Dusp5	171109	1.65	0.001	Oxidative stress response
Dual specificity phosphatase 6	Dusp6	116663	1.68	0.001	Oxidative stress response
Eukaryotic translation initiation factor 2, subunit 1	Eif2s1	54318	1.42	0.004	Apoptosis
Enolase 1, alpha	Eno1	24333	1.59	0.000	Glycolysis
Epiregulin	Ereg	59325	7.81	0.000	EGF receptor signaling
Fatty acid binding protein 2	Fabp2	25598	4.55	0.000	Unclassified
fatty acid binding protein 6, ileal (gastrotropin)	Fabp6	25440	0.12	0.012	Unclassified
farnesyl diphosphate farnesyl transferase 1	Fdft1	29580	1.55	0.008	Cholesterol biosynthesis
fibroblast growth factor receptor 2	Fgfr2	25022	0.56	0.000	Angiogenesis
fibronectin 1	Fn1	25661	2.28	0.027	Integrin
fyn-related kinase	Frk	79209	1.57	0.000	B-cell activation + Integrin + Axon guidance
growth arrest and DNA-damage-inducible 45 alpha	Gadd45a	25112	2.70	0.000	p53 +PI3kinase
growth arrest and DNA-damage-inducible 45 beta	Gadd45b	299626	2.12	0.014	p53
growth arrest specific 6	Gas6	58935	0.58	0.005	Unclassified
glucagon	Gcg	24952	6.9	0.001	Unclassified
growth differentiation factor 15	Gdf15	29455	2.97	0.007	Unclassified
ghrelin precursor	Ghrl	59301	0.66	0.014	Unclassified
glutamate oxaloacetate transaminase 2	Got2	25721	1.56	0.001	Asparagine and aspartate biosynthesis
glycogen synthase kinase 3 alpha	Gsk3a	50686	1.89	0.001	Insulin IGF PKB +Angiogenesis + Interleukin + PI3Kinase + Hedgehog signaling
glutathione S-transferase Yc2 subunit	Gsta5	494500	10.6	0.000	Unclassified
guanylate cyclase activator 2b	Guca2b	64055	1.51	0.008	Unclassified
hemopoietic cell kinase	Hck	25734	0.58	0.001	Parkinson disease + Angiogenesis = Integrin + Interleukin
hairy and enhancer of split 1 (Drosophila)	Hes1	29577	1.44	0.003	Notch signaling
hypoxia inducible factor 1, alpha subunit	Hif1a	29560	1.59	0.000	Angiogenesis
heat shock 70kDa protein 5 (glucose-regulated protein)	Hspa5	25617	1.63	0.000	Parkinson disease
Isocitrate dehydrogenase 2 (NADP+)	Idh2	361596	1.52	0.003	Tricarboxylic acid
isopentenyl-diphosphate delta isomerase	Idi1	89784	2.23	0.000	Cholesterol biosynthesis
interleukin 15	Il15	25670	0.69	0.006	Interleukin
interleukin 1 alpha	Il1a	24493	5.03	0.000	Interleukin
intersectin 1	Itsn1	29491	2.06	0.008	Unclassified
Jun-B oncogene	Junb	24517	2.38	0.000	TGF Beta
leukotriene A4 hydrolase	Lta4h	299732	1.5	0.000	Unclassified
leukotriene C4 synthase	Ltc4s	114097	0.57	0.000	Inflammation-mediated chemokine & cytokine
mitogen activated protein kinase 3	Mapk3	50689	1.51	0.005	Inflammation-mediated chemokine & cytokine + B-cell activation +Parkinson disease +Apoptosis + Integrin + Leukotriene
muscle and microspikes RAS	Mras	25482	3.72	0.000	Integrin
mevalonate (diphospho) decarboxylase	Mvd	81726	2.21	0.004	Cholesterol biosynthesis
nuclear factor of kappa light chain gene enhancer in B-cells inhibitor, beta	Nfkbib	81525	1.41	0.001	Apoptosis + Toll-like receptor
nuclear receptor subfamily 1, group D, member 1	Nr1d1	252917	2.58	0.04	Circadian clock system
platelet derived growth factor, alpha	Pdgfa	25266	2.10	0.000	Unclassified
pyridoxal (pyridoxine, vitamin B6) kinase	Pdxk	83578	2.97	0.004	Pyridoxal phosphate salvage
phospholipase C, gamma 2	Plcg2	29337	0.59	0.000	Inflammation-mediated chemokine & cytokine + B-cell activation + Angiogenesis + PDGF signaling + VEGF signaling
phospholipase D1	Pld1	25096	1.50	0.003	Angiogenesis + Ras
pleckstrin homology domain containing, family G (with RhoGef domain) member 5	Plekhg5	310999	0.52	0.004	Cytoskeleton + Axon guidance
pancreatic polypeptide	Ppy	24677	0.43	0.01	Unclassified
presenilin 2	Psen2	81751	2.07	0.03	Notch signaling + Alzheimer disease
proteaseome (prosome, macropain) 28 subunit, 3	Psme3	287716	1.54	0.000	Cell cycle
peptide YY (mapped)	Pyy	287730	1.62	0.001	Unclassified
RAB11a, member RAS oncogene family	Rab11a	81830	1.55	0.000	Huntington disease
RAB8B, member RAS oncogene family	Rab8b	266688	1.42	0.000	TGF beta signaling
RAP2B, member of RAS oncogene family	Rap2b	170923	2.16	0.000	Integrin
resistin-like gamma	Retnlg	288135	3.6	0.006	Unclassified
ras homolog gene family, member B	Rhob	64373	1.56	0.002	Inflammation-mediated chemokine & cytokine + Angiogenesis + Integrin + Axon guidance + Ras + Cytoskeleton regulation by RhoGTPase
ribosomal protein S6 kinase, polypeptide 2	Rps6kb2	361696	1.44	0.001	PDGF signaling + PI3Kinase
scavenger receptor class B, member 1;	Scarb1	25073	2.52	0.004	Unclassified
Secretogranin V	Scg5	25719	1.55	0.001	Unclassified
monocarboxylate transporter	Slc16a3	80878	2.36	0.000	Unclassified
SMAD family member 6	Smad6	367100	0.67	0.000	TGF beta signaling
MAD homolog 7 (Drosophila)	Smad7	81516	0.66	0.001	TGF beta signaling
smoothened homolog (Drosophila)	Smo	25273	2.69	0.005	Hedgehog signaling
small nuclear ribonucleoprotein polypeptide A	Snrpa	292729	1.83	0.006	mRNA splicing
synaptotagmin 12	Syt12	191595	0.31	0.003	Unclassified
toll-like receptor 3	Tlr3	364594	0.74	0.007	Toll-like receptor
tumor necrosis factor receptor superfamily, member 1a	Tnfrsf1a	25625	1.64	0.000	Apoptosis
TOX high mobility group box family member 4	Tox4	286990	1.93	0.006	Nucleoside, nucleotide and nucleic acid metabolism
vascular endothelial growth factor A	Vegfa	83785	2.82	0.000	Angiogenesis + VEGF signaling
tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide	Ywhag	56010	1.85	0.000	FGF signaling + PI3Kinase

¹One gene did not amplify on the 96 well LDA panel,platforms and, therefore, only 93 of 94 test genes are reported in tables 3 through 5. The gene was Cga (Gene ID 116700), glycoprotein hormones, alpha subunit, with FC 0.390 and p value 0.02. Two genes were used as controls and not listed in the tables.

²All genes in table are currently (July 2011) recognized as genes at the NCBI website.