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Table 4 Gene sets highly ranked across platforms. For each platform, gene sets were ranked by their association with the phenotype under study, using the p-value from the global test. Displayed are those gene sets that rank highly in the majority of platforms; for GO sets, the sum of the highest three (out of five) ranks had to be below 100; for KEGG sets, the sum of the highest four (out of five) ranks had to be below 100. Columns 1 and 2 display GO/KEGG IDs and names of the gene sets (in parentheses: GO classification: BP = biological process; MF = molecular function). Columns 3 to 7 display the ranks of the gene sets for each of the platforms.

From: Can subtle changes in gene expression be consistently detected with different microarray platforms?

GENE SET ID

Name

ABI

AFF

AGL

ILL

LGTC

GO

      

GO:0007214

gamma-aminobutyric acid signaling pathway (BP)

232

46

23

26

33

GO:0004890

GABA-A receptor activity (MF)

248

42

11

13

48

GO:0016917

GABA receptor activity (MF)

283

40

14

12

52

GO:0030594

neurotransmitter receptor activity (MF)

433

23

2

2

166

GO:0042165

neurotransmitter binding (MF)

474

22

1

1

174

GO:0006821

chloride transport (BP)

853

17

3

22

21

GO:0015698

inorganic anion transport (BP)

1022

7

21

33

76

GO:0005230

extracellular ligand-gated ion channel activity (MF)

1672

29

10

17

91

GO:0006820

anion transport (BP)

1801

8

33

34

98

GO:0015276

ligand-gated ion channel activity (MF)

1900

20

4

11

175

GO:0050900

leukocyte migration (BP)

13

898

12

69

1726

KEGG

      

4080

Neuroactive ligand-receptor interaction

25

1

3

2

10

4512

ECM-receptor interaction

18

9

21

16

33

2010

ABC transporters – General

27

3

15

4

53

4660

T cell receptor signaling pathway

23

16

57

8

31

760

Nicotinate and nicotinamide metabolism

58

8

4

161

20

3030

DNA polymerase

9

11

12

24

138

4514

Cell adhesion molecules (CAMs)

39

13

23

17

115

900

Terpenoid biosynthesis

13

12

54

19

62

4640

Hematopoietic cell lineage

64

4

22

9

76