Microarray analysis of peripheral blood lymphocytes from ALS patients and the SAFE detection of the KEGG ALS pathway

Jean-Luc C Mougeot; Zhen Li; Andrea E Price; Fred A Wright; Benjamin R Brooks

doi:10.1186/1755-8794-4-74

Table 6 Genes differentially expressed in lymphocytes from ALS patients compared to healthy controls and contributing to the KEGG ALS pathway as determined by SAFE

From: Microarray analysis of peripheral blood lymphocytes from ALS patients and the SAFE detection of the KEGG ALS pathway

^αEntrez Gene ID	^βSymbol	^γDescription	^δSAFE	^εPS/PT	^λFC	^κEffect in ALS			^τLR
57679	ALS2	amyotrophic lateral sclerosis 2 (juvenile)	-	n.d.	<	↓	-	[11586298]	n.d.
317	APAF1	apoptotic peptidase activating factor 1	-	n.d.	<	↑	-	[16046141]	n.d.
572	BAD	BCL2-associated agonist of cell death	+	1/1	1.38 ↓	↑	-	[19043451]	+
581	BAX	BCL2-associated X protein	+	10/11	1.11 ↓	↑	-	[17171827]	+
596	BCL2	apoptosis regulator B-cell CLL/lymphoma 2	+	10/11	1.07 ↑	↑	+	[20460269]	+
598	BCL2L1	inhibitor of cell death BCL2-like 1	-	n.d.	<	↑	+	[12097494]	n.d.
637	BID	BH3 interacting domain death agonist	+	1/2	<	↑	-	[12213439]	n.d.
834	CASP1	caspase 1, apoptosis-related cysteine peptidase	+	1/1	1.54 ↑	↑	-	[10764647]	-
836	CASP3	caspase 3, apoptosis-related cysteine peptidase	+	10/10	1.20 ↑	↑	-	[10764647]	-
842	CASP9	caspase 9, apoptosis-related cysteine peptidase	-	2/2	1.07 ↑	↑	-	[14657037]	-
847	CAT	catalase (heme containing)	+	1/1	1.46 ↑	↑	+	[8731383]	+
9973	CCS	copper chaperone for superoxide dismutase	-	1/1	1.08 ↓	↓	-	[17389365]	-
11261	CHP	calcineurin B homolog	+	1/1	1.16 ↑	↑	+	[11350981]	+
63928	CHP2	calcineurin B homologous protein 2	-	n.d.	<	↑	+	[12226101]	n.d.
54205	CYCS	cytochrome c, somatic	+	2/3	1.10 ↑	↓	-	[17454840]	+
1616	DAXX	death-domain associated protein	-	n.d.	<	↑	-	[12354397]	n.d.
79139	DERL1	degradation in endoplasmic reticulum protein 1	+	1/1	<	↑	-	[18519638]	n.d.
2876	GPX1	glutathione peroxidase 1	+	1/1	1.22 ↓	↓	-	[9335008]	-
2890	GRIA1	glutamate receptor, ionotropic, AMPA 1	-	n.d.	<	↓	-	[8981413]	n.d.
2891	GRIA2	glutamate receptor, ionotropic, AMPA 2	-	n.d.	<	↓	-	[8981413]	n.d.
2902	GRIN1	glutamate receptor, ionotropic, N-methyl D-aspartate 1	+	2/2	1.44 ↓	↓	-	[1320444]	-
2903	GRIN2A	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	-	n.d.	<	↓	-	[8842405]	n.d.
2904	GRIN2B	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	-	n.d.	<	↓	+	[16490316]	n.d.
2905	GRIN2C	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	-	n.d.	<	↓	+	[11717388]	n.d.
2906	GRIN2D	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	+	1/1	1.58 ↓	↑	+	[15152019]	-
5606	MAP2K3	mitogen-activated protein kinase kinase 3	+	1/1	1.34 ↓	↑	-	[17686961]	+
5608	MAP2K6	mitogen-activated protein kinase kinase 6	-	1/1	1.32 ↑	↑	-	[16219474]	-
4217	MAP3K5	mitogen-activated protein kinase kinase kinase 5	+	1/1	1.10 ↑	↑	-	[15910777]	-
5600	MAPK11	mitogen-activated protein kinase 11	-	n.d.	<	↑	-	[9218798]	n.d.
6300	MAPK12	mitogen-activated protein kinase 12	-	n.d.	<	↑	-	[9169156]	n.d.
5603	MAPK13	mitogen-activated protein kinase 13	-	n.d.	<	↑	-	[9218798]	n.d.
1432	MAPK14	mitogen-activated protein kinase 14	+	10/10	1.26 ↑	↑	-	[15910777]	-
4744	NEFH	neurofilament, heavy polypeptide	-	n.d.	<	↓	-	[7849698]	n.d.
4747	NEFL	neurofilament, light polypeptide	-	n.d.	<	↓	-	[15207859]	n.d.
4741	NEFM	neurofilament, medium polypeptide	-	n.d.	<	↓	-	[11732278]	n.d.
4842	NOS1	nitric oxide synthase 1 (neuronal)	-	n.d.	<	↑	-	[15033415]	n.d.
5530	PPP3CA	protein phosphatase 3, catalytic subunit, alpha isozyme	+	3/3	1.06 ↑	↓	-	[11701756]	+
5532	PPP3CB	protein phosphatase 3, catalytic subunit, beta isozyme	+	1/1	1.28 ↑	↓	-	[15312178]	+
5533	PPP3CC	protein phosphatase 3, catalytic subunit, gamma isozyme	+	1/1	<	↓	-	[15312178]	n.d.
5534	PPP3R1	protein phosphatase 3, regulatory subunit B, alpha	-	n.d.	<	↓	-	[11754729]	n.d.
5535	PPP3R2	protein phosphatase 3, regulatory subunit B, beta	-	n.d.	<	↓	-	[11754729]	n.d.
5630	PRPH	peripherin	-	n.d.	<	↓	-	[20363051]	n.d.
5961	PRPH2	peripherin 2	-	n.d.	<	↓	-	[8125718]	n.d.
5868	RAB5A	ras-related protein Rab-5A	+	1/1	1.11 ↓	↓	+	[11316809]	+
5879	RAC1	ras-related C3 botulinum toxin substrate 1	+	12/12	1.08 ↓	↓	-	[18219391]	-
6506	SLC1A2	sodium-dependent glutamate/aspartate transporter 2	-	n.d.	<	↑	+	[14530974]	n.d.
6647	SOD1	superoxide dismutase 1, soluble	+	11/11	1.24 ↑	↓	-	[20644736]	+
7124	TNF	tumor necrosis factor alpha	+	1/1	1.15 ↑	↑	+	[18823372]	+
7132	TNFRSF1A	tumor necrosis factor receptor superfamily, member 1A	-	n.d.	<	↑	-	[11917000]	n.d.
7133	TNFRSF1B	tumor necrosis factor receptor superfamily, member 1B	-	n.d.	<	↓	+	[11917000]	n.d.
10452	TOMM40	mitochondrial import receptor subunit TOM40 homolog	-	n.d.	<	↓	-	[20797528]	n.d.
84134	TOMM40L	mitochondrial import receptor subunit TOM40B	-	1/1	1.23 ↓	↓	-	[20797528]	-
7157	TP53	tumor protein p53	-	n.d.	<	↑	-	[8609941]	n.d.

Genes (53 in total, pseudogene CASP12 excluded) belonging to the KEGG ALS pathway (hsa05014) that describe pathogenic effects in motor neurons are defined by their official HUGO symbol. ^αEntrez Gene accession number and ^βHUGO symbol and ^γdescription are provided. ^δGenes that contribute to the KEGG ALS pathway through SAFE analysis are marked with a (+) sign and if not with a (-) sign. Number of probes significant (PS) per total number of probe signal intensity values per gene on the Agilent 4 × 44K array (PT) is shown. ^λFC is average fold change ALS (n = 11) compared to healthy controls (n = 11) considering one or more probe signal intensity values per gene, with upregulated genes indicated by (↑) and downregulated genes by (↓). Less than 1.05 fold changes are indicated by (<). ^κPMID referenced positive (+) or negative (-) effect on motor neuron survival if wild type protein activity or function is increased (↑) or normal function or activity is altered (↓). Genes that were not determined (n.d.) to contribute to the KEGG ALS pathway or with an FC < 1.05, are also referenced for known effects. ^τLymphocyte response (LR) represented by the genes contributing to the KEGG ALS pathway is shown.

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