Inflammatory Pathways in Parkinson’s Disease; A BNE Microarray Study

Table 3

Expression levels of genes validated using qPCR (in alphabetical order).

Name	Description	Function	Primers Assays	Chromosome	Microarray data			RT-qPCR data		Microarray/qPCR
					FC	𝑃 value	t-test	FC	𝑃 value	Pearson r	𝑃 value
ACTN4	Actinin, alpha 4	Regulation of actin cytoskeleton	QT00030765	19q13.2	1.88	<0.0001	0.0004	2.155	0.006	0.8744	0.0002
ASTN1	Astrotactin 1	Neuron adhesion	QT00084609	1q25.2	−1.52	<0.0001	0.0006	−1.56	0.003	0.6475	0.0067
CBLN1	Cerebellin 1 precursor	Synaptic transmission	QT00224126	16q12.1	−2.90	0.0048	0.048	−4.19	0.026	0.9745	<0.0001
CLDN11	Claudin 11	Axon ensheathment	QT00008085	3q26.2	1.62	0.0048	0.0158	1.98	0.014	0.8626	0.0001
CSF1R	Colony stimulating factor 1 receptor	Macrophage function	QT00041293	5q33.1	1.52	0.0042	0.035	1.79	0.012	0.719	0.0005
CTGF	Connective tissue growth factor	Angiogenesis	QT00052899	6q23.2	2.77	0.0001	0.003	2.79	0.032	0.9276	<0.0001
DNAH17	Dynein, axonemal, heavy polypeptide 17	Microtubule based movement	QT00065226	17q25.3	2.06	0.0007	0.01	2.32	0.025	0.8675	0.0001
DOCK10	Dedicator of cytokinesis 10	Unknown	QT00009835	2q36.2	1.58	0.0022	0.01	1.65	0.014	0.8717	<0.0001
DRD1IP	Dopamine receptor D1 interacting protein	Dopamine receptor signalling	QT00493031	10q26.3	−1.90	0.0062	0.037	−2.6	0.035	0.9471	<0.0001
ELF1	E74-like factor 1	Immune response	QT00023716	13q14.11	1.55	<0.0001	0.0076	2.21	0.044	ns	ns
GABRB1	Gamma-aminobutyric acid (GABA) A receptor, beta 1	Synaptic Transmission	QT00007455	4p12b	−1.77	<0.0001	0.0086	−2.85	0.0003	0.8406	<0.0001
GADD45B	Growth arrest and DNA-damage-inducible, beta	Myeloid differentiation primary response	QT00014084	19p13.3	−3.64	0.0001	0.047	−6.46	0.024	0.9833	<0.0001
GATA2	GATA binding protein 2	Positive regulation of angiogenesis & phagocytosis	QT00045381	3q21.3	2.13	<0.0001	0.0001	3.49	0.001	0.5965	0.0314
GJC2	Gap junction protein, gamma 2, 47 kDa	Myelination	QT01674239	1q42.13	2.25	0.0001	0.006	7.38	0.008	0.9334	<0.0001
HMGCS1	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble)	Metabolic process	QT00055531	5p12	−1.56	<0.0001	0.005	−1.84	0.019	0.8750	<0.0001
IFNGR1	Interferon gamma receptor 1	Response to virus	QT00089404	6q23.3	1.55	<0.0001	0.002	1.735	0.015	0.7461	0.0004
JUP	Junction plakoglobin	Cell-cell adhesion	QT00089166	17q21.2	1.84	<0.0001	0.00037	2.95	0.025	0.82850	0.0016
NOS3	Nitric oxide synthase 3 (endothelial cells)	Angiogenesis	QT00089033	7q36.1-36.1	1.91	0.0026	0.0139	5.05	0.002	0.8042	0.0028
NOTCH1	Notch homolog 1, translocation-associated (Drosophila)	Notch signalling	QT01005109	9q34.3	1.62	<0.0001	0.00029	1.75	0.013	0.8656	0.0006
NPTX2	Neuronal pentraxin II	Synaptic transmission	QT00001876	7q22.1	3.05	<0.0001	0.002	3.52	0.008	0.9275	<0.0001
P2RX7	Purinergic receptor P2X, ligand-gated ion channel, 7	ATP-dependent lysis of macrophages	QT00083643	12q24.31	2.20	0.0003	0.0064	3.12	0.014	0.9664	<0.0001
PHLDB1	Pleckstrin homology-like domain, family B, member 1	Unknown	QT00083601	11q23.3	1.52	0.0013	0.0153	1.75	0.023	0.6180	0.0107
PLEKHA5	Pleckstrin homology domain containing, family A member 5	Phosphatidylinositol binding	QT00045605	12p12.3	−1.57	<0.0001	0.005	−2.3	0.014	0.8098	0.0003
PML	Promyelocytic leukemia	PML body organisation	QT01841945	15q24.1	1.51	0.0023	0.0067	1.69	0.014	0.8626	0.0006
SEPT3	Septin 3 (neuronal specific)	Unknown	QT00020111	22q13.2	−1.57	0.0014	0.01	−1.87	0.042	0.8476	<0.0001
SGK1	Serum/glucocorticoid regulated kinase	Response to stress	QT00041293	6q23.2	1.74	0.0004	0.0029	2.07	0.002	0.587	<0.0001
SNCA	Synuclein, alpha	Dopamine metabolism	QT00035903	4q21	−1.48	0.084 ns	ns	−1.34	0.35 ns	ns	ns
SNCAIP1	Synuclein, alpha interacting protein	Dopamine metabolism	QT00054320	5q23.2	−1.62	0.0012	0.026	−1.87	0.055^∧	0.8388	0.0012
STAT2	Signal transducer and activator of transcription 2, 113 kDa	Response to virus	QT00095704	12q13.2	1.93	<0.0001	0.00024	2.10	0.011	0.7973	0.0002
TH	Tyrosine hydroxylase	Dopamine biosynthesis	QT00067221	11p15.5	−3.10	<0.0001	0.0035	−3.27	0.043	0.9016	<0.0001
TJAP1	Tight junction associated protein 1	Tight junction function	QT00091903	6p21.1	2.03	<0.0001	0.00079	1.97	0.007	0.7145	0.0041
TNFRSF14	Tumour necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	Immune response	QT00082432	1p36.32	1.94	<0.0001	<0.0001	2.035	0.012	ns	ns
ZBTB16	Zinc finger and BTB domain containing 46	Cell cycle progression	QT00029960	11q23.2	1.67	0.0011	0.0105	1.785	0.032	0.923	<0.0001

^∧ = Trend; ns: not significant
Microarray data: Rosetta error model + Student t-test (2-tailed, unequal variance)
qPCR: Student t-test (2-tailed, unequal variance)
Correlation microarray and qPCR data: Pearson correlation test.