Table 2

Significantly enriched classes arising both in genes higher in A549 cell cultures over tumors and in genes higher in U118 cell cultures over tumors (p < 0.05 in both sets)
Category
 Term
 Gene count in A549 set of 223
 Gene count in U118 set of 256
 Gene count in entire set of 5,682
 p-value A549 set
 p-value U118 set
GO term annotation (0.95 terms expected, found 46)
Biological process
 Alcohol metabolism
 10
 15
 110
 1.07E-02
 1.06E-04
Biological process
 Aromatic compound metabolism
 7
 6
 23
 1.87E-05
 4.16E-04
Biological process
 Biosynthesis
 31
 27
 330
 3.88E-06
 1.69E-03
Biological process
 Cell cycle
 31
 33
 327
 3.20E-06
 8.11E-06
Biological process
 Cell proliferation
 36
 39
 535
 7.98E-04
 1.53E-03
Biological process
 Cytokinesis
 8
 6
 39
 1.06E-04
 7.36E-03
Biological process
 DNA metabolism
 16
 12
 120
 1.52E-05
 7.46E-03
Biological process
 DNA replication
 13
 10
 81
 1.30E-05
 3.22E-03
Biological process
 G1/S transition of mitotic cell cycle
 5
 7
 39
 1.73E-02
 1.55E-03
Biological process
 Metabolism
 108
 134
 2278
 6.12E-03
 3.34E-05
Biological process
 Mitotic cell cycle
 9
 10
 54
 2.14E-04
 1.20E-04
Biological process
 Nucleotide biosynthesis
 10
 5
 31
 1.52E-07
 1.16E-02
Biological process
 Regulation of CDK activity
 5
 6
 23
 1.68E-03
 4.16E-04
Biological process
 Tricarboxylic acid cycle
 3
 5
 12
 1.01E-02
 1.09E-04
Molecular function
 ATP binding activity
 29
 33
 425
 2.18E-03
 1.28E-03
Molecular function
 Cyclin-dependent protein kinase activity
 6
 8
 25
 3.23E-04
 8.44E-06
Molecular function
 Enzyme activity
 90
 109
 1466
 8.76E-07
 1.70E-09
Molecular function
 Ligase activity
 14
 11
 72
 5.40E-07
 3.28E-04
Molecular function
 Lyase activity
 8
 8
 75
 8.69E-03
 1.88E-02
Molecular function
 Nucleotide binding activity
 40
 42
 564
 1.28E-04
 6.40E-04






MeSH term association (2.2 terms expected, found 37)
Anatomy
 Intracellular membranes
 21
 30
 344
 2.79E-02
 3.20E-04
Anatomy
 Mitochondria
 38
 52
 607
 2.17E-03
 2.46E-06
Biological sciences
 Active transport, Cell nucleus
 23
 23
 329
 4.68E-03
 2.26E-02
Biological sciences
 Cell cycle
 62
 66
 980
 4.19E-05
 2.82E-04
Biological sciences
 DNA replication
 30
 33
 440
 1.84E-03
 2.28E-03
Biological sciences
 Genes, lethal
 17
 16
 211
 3.61E-03
 2.78E-02
Biological sciences
 Mitosis
 28
 37
 484
 2.30E-02
 8.57E-04
Biological sciences
 Mutagenesis
 52
 55
 940
 4.84E-03
 2.07E-02
Biological sciences
 Oxidative stress
 30
 36
 454
 2.98E-03
 5.13E-04
Biological sciences
 S phase
 21
 22
 272
 2.12E-03
 5.18E-03
Chemicals and drugs
 Acetyl coenzyme A
 4
 4
 24
 1.32E-02
 2.10E-02
Chemicals and drugs
 Adenosinetriphosphatase
 30
 36
 416
 7.50E-04
 9.02E-05
Chemicals and drugs
 Antineoplastic agents
 49
 55
 897
 8.09E-03
 8.39E-03
Chemicals and drugs
 Cyclin B
 10
 15
 101
 5.96E-03
 3.87E-05
Chemicals and drugs
 Cyclin-dependent kinases
 21
 30
 336
 2.22E-02
 2.12E-04
Chemicals and drugs
 Cysteine endopeptidases
 26
 29
 418
 1.21E-02
 1.22E-02
Chemicals and drugs
 Multienzyme complexes
 35
 35
 512
 7.14E-04
 7.58E-03
Chemicals and drugs
 Phosphoglucomutase
 5
 6
 30
 5.68E-03
 1.88E-03
Chemicals and drugs
 RNA nucleotidyltransferases
 5
 5
 33
 8.60E-03
 1.51E-02
Diseases
 Carcinoma in situ
 6
 7
 55
 1.99E-02
 1.11E-02

Creighton et al. Genome Biology 2003 4:R46   doi:10.1186/gb-2003-4-7-r46

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