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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 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.
  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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