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Table 3 SAFE gene ontology pathways related to Biological Processes affected in peripheral blood lymphocytes from ALS patients

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

αPathway βSizes δq-value εGO Term
DNA Metabolism
GO:0006310 54/71 0 DNA recombination
GO:0006302 27/50 0.003 double-strand break repair
GO:0000718 12/21 0.0414 nucleotide-excision repair DNA damage removal
ER and Golgi
GO:0006895 6/7 0.0071 Golgi to endosome transport
GO:0006888 26/43 0.1127 ER to Golgi vesicle-mediated transport
GO:0006904 10/19 0.0071 vesicle docking during exocytosis
GO:0006892 11/41 0.0471 post-Golgi vesicle-mediated transport
GO:0007041 7/6 0.1885 lysosomal transport
Mitochondrial Function
GO:0022904 53/98 0.0558 mitochondrial ATP synthesis coupled electron transport
    respiratory electron transport chain
GO:0006120 44/43 0.0523 mitochondrial electron transport NADH to ubiquinone
GO:0006626 17/25 0.0972 protein targeting to mitochondrion
GO:0006119 81/8 0.1 oxidative phosphorylation
Neurological Function
GO:0010001 8/13 0.1 glial cell differentiation
GO:0042552 8/30 0.1138 myelination
Oxidation
GO:0019395 19/6 0.2252 fatty acid oxidation
RNA Metabolism
GO:0000387 25/26 0.003 spliceosomal snRNP biogenesis
GO:0033119 10/3 0.0071 negative regulation of RNA splicing
GO:0051028 81/62 0.0644 mRNA transport
PTM
GO:0070206 7/7 0 protein trimerization
GO:0018279 8/47 0.0071 protein amino acid N-linked glycosylation via asparagine
GO:0051262 10/12 0.0644 protein tetramerization
GO:0006465 7/9 0.0835 signal peptide processing
GO:0045116 8/7 0.0644 protein neddylation
GO:0016925 15/11 0.0627 protein sumoylation
UPS
GO:0051443 62/6 0.0644 positive regulation of ubiquitin-protein ligase activity
GO:0051444 59/4 0.0644 negative regulation of ubiquitin-protein ligase activity
GO:0043161 79/43 0.0644 proteasomal ubiquitin-dependent protein catabolic process
Viral Infection
GO:0019047 11/8 0.044 provirus integration
GO:0019059 18/12 0.0852 initiation of viral infection
GO:0019058 41/92 0.0644 viral infectious cycle
  1. αGene ontology (GO) pathway identities for biological processes and βnumber of probes represented on the 4 × 44K human genome array per GO group of directly associated proteins is shown (note: one gene may be represented by different or redundant probes on the array). γFDR (q-value) at significance level p < 0.25 (25%) was determined by bootstrapping following SAFE analysis. δThe table shows partial listing of representative significant εGO categories associated with biological processes (30 among 99). UPS is ubiquitin/proteasome system, PTM is post-translational modification, and ER is endoplasmic reticulum.