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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.
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BMC Medical Genomics

ISSN: 1755-8794

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