Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by - Regularization and Data Reduction
Table 2
Functional gene classes.
Biological group(1)
Functional class(2)
GO number(3)
no. of probesets(4)
error(%)(5)
Hypoxia
Angiogenesis
GO: 1525
257
39
GO: 6915
1366
Cell proliferation
GO: 8283
1406
28
DNA repair
GO: 6281
567
44
Glucose import
GO: 46323
10
89
Glucose Transport
GO: 15758
48
33
GO: 6096
128
Iron ion homeostasis
GO: 6879
65
39
Notch signaling pathway
GO: 7219
134
44
GO: 6119
154
Oxygen transport
GO: 15671
38
28
Regulation of pH
GO: 6885
41
72
Response to hypoxia
GO: 1666
32
28
MYCN
G1-S transition of mitotic cell cycle
GO: 82
62
50
Proteasomal ubiquitin-dependent protein catabolism
GO: 43161
33
50
Protein folding
GO: 6457
601
22
Ribosome biogenesis and assembly
GO: 42254
170
28
Structural constituent of ribosome
GO: 3735
549
44
Translational elongation
GO: 6414
56
56
Translational initiation
GO: 6413
173
44
Neuroblastoma
Axon guidance
GO: 7411
109
50
Axonal fasciculation
GO: 7412
4
100
Cell cycle arrest
GO: 7050
210
39
Dendrite morphogenesis
GO: 16358
12
72
Glial cell migration
GO: 8347
2
100
Inactivation of MAPK activity
GO: 188
50
44
Nervous system development
GO: 7399
1284
22
Neuron migration
GO: 1764
7
94
Positive regulation of neuron differentiation
GO: 45666
6
100
Regulation of axon extension
GO: 30516
14
100
Regulation of G-protein coupled receptor protein signaling pathway
GO: 8277
88
39
Regulation of neuronal synaptic plasticity
GO: 48168
8
100
Regulation of neurotransmitter secretion
GO: 46928
11
61
Synaptic vesicle transporter
GO: 48489
36
72
Vesicle organization and biogenesis
GO: 16050
6
44
(1)Functional classes were clustered into three main biological groups depending on the characteristic of the experimental system and accordingly to the literature. (2)Defined according to the predetermined pathways and functional categories annotated by the Gene Ontology project [26]. (3) Gene Ontology ID [26]. (4)Number of probesets present in Affymetrix HG-U133 Plus 2.0 GeneChip belonging to the selected classes. (5)Leave-one-out error, as calculated by regularization by setting and frequency score = 50. classes with leave-one-out error 20%.
