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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

Ï„LR

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.

  1. 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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BMC Medical Genomics

ISSN: 1755-8794

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