Table 2

Differentially regulated GO categories

Up-regulated GO categories

GO ID

GO Name

GO Type

Number Changed

Number Measured

Percent Changed

z Score

corrected P


6955

immune response

BP

106

346

30.64

7.84

0

9607

response to biotic stimulus

BP

130

456

28.51

7.77

0

6952

defense response

BP

113

381

29.66

7.71

0

50874

organismal physiological process

BP

208

859

24.21

7.30

0

50896

response to stimulus

BP

215

941

22.85

6.45

0

43207

response to external biotic stimulus

BP

71

235

30.21

6.24

0

9613

response to pest\, pathogen or parasite

BP

69

228

30.26

6.16

0

9605

response to external stimulus

BP

134

563

23.80

5.51

0.01

4871

signal transducer activity

MF

251

1199

20.93

5.44

0.011

9596

detection of pest\, pathogen or parasite

BP

5

5

100.00

5.19

0.047


2453

probes met the [fold-change]>=1.2 criterion.

1782

probes meeting the filter linked to an Ensembl ID.

1323

genes meeting the criterion linked to a GO term.

The z score is based on an N of 8457 and an R of 1323 distinct genes in the GO.


Down-regulated GO categories

GO ID

GO Name

GO Type

Number Changed

Number Measured

Percent Changed

z Score

corrected P


15077

monovalent inorganic cation transporter activity

MF

86

120

71.67

13.88

0

15078

hydrogen ion transporter activity

MF

80

111

72.07

13.44

0

15399

primary active transporter activity

MF

88

131

67.18

13.23

0

16655

oxidoreductase activity\, acting on NADH or NADPH\, quinone or similar compound as acceptor

MF

37

42

88.10

10.81

0

5739

mitochondrion

CC

186

459

40.52

10.78

0

3954

NADH dehydrogenase activity

MF

34

38

89.47

10.49

0

6119

oxidative phosphorylation

BP

47

64

73.44

10.45

0

50136

NADH dehydrogenase (quinone) activity

MF

33

37

89.19

10.30

0

8137

NADH dehydrogenase (ubiquinone) activity

MF

33

37

89.19

10.30

0

16651

oxidoreductase activity\, acting on NADH or NADPH

MF

43

57

75.44

10.23

0

15081

sodium ion transporter activity

MF

34

40

85.00

10.06

0

19866

inner membrane

CC

62

114

54.39

8.94

0

42775

ATP synthesis coupled electron transport (sensu Eukaryota)

BP

22

24

91.67

8.59

0

5737

cytoplasm

CC

547

1987

27.53

8.58

0

6091

generation of precursor metabolites and energy

BP

143

375

38.13

8.52

0

8324

cation transporter activity

MF

127

324

39.20

8.38

0

42773

ATP synthesis coupled electron transport

BP

22

25

88.00

8.32

0

5740

mitochondrial membrane

CC

59

115

51.30

8.15

0

46873

metal ion transporter activity

MF

42

70

60.00

8.15

0

15075

ion transporter activity

MF

146

397

36.78

8.10

0

5386

carrier activity

MF

109

271

40.22

8.06

0

6120

mitochondrial electron transport\, NADH to ubiquinone

BP

19

21

90.48

7.90

0

5743

mitochondrial inner membrane

CC

48

89

53.93

7.78

0

6096

glycolysis

BP

22

30

73.33

7.13

0

6754

ATP biosynthesis

BP

26

41

63.41

6.77

0

6753

nucleoside phosphate metabolism

BP

26

41

63.41

6.77

0

9206

purine ribonucleoside triphosphate biosynthesis

BP

30

51

58.82

6.74

0

9145

purine nucleoside triphosphate biosynthesis

BP

30

51

58.82

6.74

0

9201

ribonucleoside triphosphate biosynthesis

BP

30

51

58.82

6.74

0

6092

main pathways of carbohydrate metabolism

BP

35

64

54.69

6.74

0

15992

proton transport

BP

31

54

57.41

6.68

0

16818

hydrolase activity\, acting on acid anhydrides\, in phosphorus-containing anhydrides

MF

124

358

34.64

6.65

0

16817

hydrolase activity\, acting on acid anhydrides

MF

124

358

34.64

6.65

0

9142

nucleoside triphosphate biosynthesis

BP

30

52

57.69

6.60

0

15405

P-P-bond-hydrolysis-driven transporter activity

MF

36

68

52.94

6.59

0

9199

ribonucleoside triphosphate metabolism

BP

31

55

56.36

6.55

0

9144

purine nucleoside triphosphate metabolism

BP

31

55

56.36

6.55

0

6818

hydrogen transport

BP

31

55

56.36

6.55

0

9205

purine ribonucleoside triphosphate metabolism

BP

31

55

56.36

6.55

0

46034

ATP metabolism

BP

27

45

60.00

6.52

0

16462

pyrophosphatase activity

MF

122

356

34.27

6.45

0

46961

hydrogen-transporting ATPase activity\, rotational mechanism

MF

23

36

63.89

6.41

0

16469

proton-transporting two-sector ATPase complex

CC

23

36

63.89

6.41

0

9152

purine ribonucleotide biosynthesis

BP

33

62

53.23

6.34

0

9141

nucleoside triphosphate metabolism

BP

31

57

54.39

6.30

0

15985

energy coupled proton transport\, down electrochemical gradient

BP

23

37

62.16

6.24

0

6007

glucose catabolism

BP

23

37

62.16

6.24

0

15986

ATP synthesis coupled proton transport

BP

23

37

62.16

6.24

0

15980

energy derivation by oxidation of organic compounds

BP

46

101

45.54

6.20

0

5489

electron transporter activity

MF

67

168

39.88

6.20

0

45259

proton-transporting ATP synthase complex

CC

10

10

100.00

6.19

0

45255

hydrogen-translocating F-type ATPase complex

CC

10

10

100.00

6.19

0

5753

proton-transporting ATP synthase complex (sensu Eukaryota)

CC

10

10

100.00

6.19

0

46933

hydrogen-transporting ATP synthase activity\, rotational mechanism

MF

22

35

62.86

6.17

0

42625

ATPase activity\, coupled to transmembrane movement of ions

MF

32

61

52.46

6.14

0

19829

cation-transporting ATPase activity

MF

23

38

60.53

6.07

0

17111

nucleoside-triphosphatase activity

MF

114

338

33.73

6.03

0

9150

purine ribonucleotide metabolism

BP

33

65

50.77

6.01

0

6164

purine nucleotide biosynthesis

BP

33

65

50.77

6.01

0

45298

tubulin

BP

15

20

75.00

6.00

0

46785

microtubule polymerization

CC

15

20

75.00

6.00

0

9260

ribonucleotide biosynthesis

BP

33

66

50.00

5.90

0

31109

microtubule polymerization or depolymerization

BP

17

25

68.00

5.84

0

9259

ribonucleotide metabolism

BP

34

70

48.57

5.78

0

46164

alcohol catabolism

BP

23

40

57.50

5.76

0

46365

monosaccharide catabolism

BP

23

40

57.50

5.76

0

19320

hexose catabolism

BP

23

40

57.50

5.76

0

6752

group transfer coenzyme metabolism

BP

27

51

52.94

5.70

0

6163

purine nucleotide metabolism

BP

33

68

48.53

5.69

0

15002

heme-copper terminal oxidase activity

MF

13

17

76.47

5.68

0

16676

oxidoreductase activity\, acting on heme group of donors\, oxygen as acceptor

MF

13

17

76.47

5.68

0

16675

oxidoreductase activity\, acting on heme group of donors

MF

13

17

76.47

5.68

0

4129

cytochrome-c oxidase activity

MF

13

17

76.47

5.68

0

6732

coenzyme metabolism

BP

45

107

42.06

5.49

0

42626

ATPase activity\, coupled to transmembrane movement of substances

MF

36

79

45.57

5.48

0

16820

hydrolase activity\, acting on acid anhydrides\, catalyzing transmembrane movement of substances

MF

36

79

45.57

5.48

0

43234

protein complex

CC

313

1175

26.64

5.41

0

51186

cofactor metabolism

BP

50

125

40.00

5.36

0

6006

glucose metabolism

BP

27

54

50.00

5.33

0

5215

transporter activity

MF

240

871

27.55

5.27

0

45333

cellular respiration

BP

17

28

60.71

5.23

0

51258

protein polymerization

BP

18

31

58.06

5.14

0.002

226

microtubule cytoskeleton organization and biogenesis

BP

25

50

50.00

5.13

0.004

31090

organelle membrane

CC

89

270

32.96

5.05

0.004

7017

microtubule-based process

BP

38

93

40.86

4.82

0.01

502

proteasome complex (sensu Eukaryota)

CC

18

33

54.55

4.81

0.016

16052

carbohydrate catabolism

BP

24

50

48.00

4.78

0.025

44275

cellular carbohydrate catabolism

BP

24

50

48.00

4.78

0.025

9117

nucleotide metabolism

BP

48

128

37.50

4.73

0.026

6118

electron transport

BP

73

220

33.18

4.63

0.043

3924

GTPase activity

MF

44

116

37.93

4.61

0.043

16491

oxidoreductase activity

MF

115

383

30.03

4.61

0.044

5829

cytosol

CC

69

207

33.33

4.54

0.045

9165

nucleotide biosynthesis

BP

38

97

39.18

4.52

0.045


3059

probes met the [fold-change]<=(1/1.2) criterion.

2522

probes meeting the filter linked to an Ensembl ID.

1751

genes meeting the criterion linked to a GO term.

The z score is based on an N of 8457 and an R of 1751 distinct genes in the GO.


Shown are all GO nodes differentially regulated between SALS motor-cortex-patient samples and controls for the comprehensive dataset. Of 19,431 probes in the dataset, 8,457 were linked to a GO term. Nodes are sorted by up- or down-regulation (top and bottom sub-tables, respectively), then sorted by corrected P value (lowest first) and z value (highest first). CC – cellular component; MF – molecular function; BP – biological process

Lederer et al. BMC Genomics 2007 8:26   doi:10.1186/1471-2164-8-26

Open Data