Table 3

Gene Ontology Analysis

Under-represented Genes


Ontology

Rank

GO.ID

Term

Annotated

Significant

Expected

Rank in classic

classic

elim

weight


BP

1

GO:0006099

tricarboxylic acid cycle

41

6

0.23

1

9.7e-08

9.7e-08

9.7e-08

2

GO:0045900

negative regulation of translational elongation

6

3

0.03

10

3.3e-06

3.3e-06

3.3e-06

3

GO:0046500

S-adenosylmethionine metabolic process

7

3

0.04

12

5.7e-06

5.7e-06

5.7e-06

4

GO:0006446

regulation of translational initiation

70

5

0.39

19

4.3e-05

4.3e-05

4.3e-05

5

GO:0006614

SRP-dependent cotranslational protein targeting to membrane

13

3

0.07

20

4.5e-05

4.5e-05

4.5e-05

6

GO:0007021

tubulin complex assembly

5

2

0.03

31

0.00030

0.00030

0.00030

7

GO:0046498

S-adenosylhomocysteine metabolic process

5

2

0.03

32

0.00030

0.00030

0.00030

8

GO:0030091

protein repair

6

2

0.03

33

0.00045

0.00045

0.00045

9

GO:0006425

glutaminyl-tRNA aminoacylation

1

1

0.01

51

0.00554

0.00554

0.00554

10

GO:0006430

lysyl-tRNA aminoacylation

1

1

0.01

52

0.00554

0.00554

0.00554

11

GO:0043393

regulation of protein binding

25

2

0.14

54

0.00839

0.00839

0.00839


MF

1

GO:0000104

succinate dehydrogenase activity

8

5

0.04

1

2.4e-10

2.4e-10

2.4e-10

2

GO:0005047

signal recognition particle binding

7

3

0.04

3

5.4e-06

5.4e-06

5.4e-06

3

GO:0045182

translation regulator activity

211

8

1.15

4

2.1e-05

0.27124

2.1e-05

4

GO:0008312

7 S RNA binding

14

3

0.08

5

5.5e-05

5.5e-05

5.5e-05

5

GO:0008119

thiopurine S-methyltransferase activity

3

2

0.02

7

8.8e-05

8.8e-05

8.8e-05

6

GO:0003924

GTPase activity

328

8

1.79

8

0.00044

0.00044

0.00044

7

GO:0004719

protein-L-isoaspartate (D-aspartate) O-methyltransferase activity

10

2

0.05

16

0.00129

0.00129

0.00129

8

GO:0005525

GTP binding

592

10

3.22

19

0.00150

0.00150

0.00150

9

GO:0009055

electron carrier activity

349

7

1.90

22

0.00304

0.00304

0.00304

10

GO:0004819

glutamine-tRNA ligase activity

1

1

0.01

26

0.00544

0.00544

0.00544

11

GO:0004824

lysine-tRNA ligase activity

1

1

0.01

27

0.00544

0.00544

0.00544

12

GO:0003723

RNA binding

1269

17

6.91

10

0.00052

0.00680

0.00680


CC

1

GO:0005786

signal recognition particle, endoplasmic reticulum targeting

15

4

0.08

3

1.2e-06

1.2e-06

1.2e-06

2

GO:0005785

signal recognition particle receptor complex

7

3

0.04

5

6.0e-06

6.0e-06

6.0e-06

3

GO:0005853

eukaryotic translation elongation factor 1 complex

17

3

0.10

11

0.00011

0.00011

0.00011

4

GO:0002079

inner acrosomal membrane

4

2

0.02

13

0.00019

0.00019

0.00019

5

GO:0042589

zymogen granule membrane

5

2

0.03

16

0.00031

0.00031

0.00031

6

GO:0008290

F-actin capping protein complex

7

2

0.04

24

0.00065

0.00065

0.00065

7

GO:0005743

mitochondrial inner membrane

391

11

2.20

6

1.3e-05

1.3e-05

0.00263

8

GO:0044444

cytoplasmic part

6340

68

35.62

1

1.5e-09

0.01111

0.00499

9

GO:0045273

respiratory chain complex II

3

2

0.02

10

9.4e-05

9.4e-05

0.00558

10

GO:0005759

mitochondrial matrix

295

6

1.66

30

0.00652

0.00652

0.00652


Over-represented Genes


Ontology

Rank

GO.ID

Term

Annotated

Significant

Expected

Rank in classic

classic

elim

weight


BP

1

GO:0018279

protein amino acid N-linked glycosylation via asparagine

20

2

0.02

1

0.00013

0.00013

0.00013

2

GO:0006414

translational elongation

253

3

0.22

3

0.00127

0.00127

0.00127

3

GO:0000722

telomere maintenance via recombination

2

1

0.00

5

0.00173

0.00173

0.00173

4

GO:0009446

putrescine biosynthetic process

2

1

0.00

6

0.00173

0.00173

0.00173

5

GO:0051258

protein polymerization

106

2

0.09

8

0.00374

0.00374

0.00374

6

GO:0008295

spermidine biosynthetic process

6

1

0.01

9

0.00519

0.00519

0.00519

7

GO:0007094

mitotic cell cycle spindle assembly checkpoint

8

1

0.01

11

0.00691

0.00691

0.00691

8

GO:0007018

microtubule-based movement

157

2

0.14

13

0.00802

0.00802

0.00802

9

GO:0015937

coenzyme A biosynthetic process

10

1

0.01

15

0.00863

0.00863

0.00863


MF

1

GO:0004579

dolichyl-diphosphooligosaccharide-protein glycotransferase activity

19

2

0.02

1

0.00014

0.00014

0.00014

2

GO:0008783

agmatinase activity

2

1

0.00

3

0.00187

0.00187

0.00187

3

GO:0005198

structural molecule activity

1149

5

1.08

4

0.00359

0.13592

0.00359

4

GO:0004594

pantothenate kinase activity

7

1

0.01

6

0.00654

0.00654

0.00654

5

GO:0003720

telomerase activity

8

1

0.01

7

0.00747

0.00747

0.00747


CC

1

GO:0008250

oligosaccharyl transferase complex

20

2

0.02

1

0.00013

0.00013

0.00013

2

GO:0005840

ribosome

407

3

0.35

13

0.00493

0.00493

0.00493


The GO analysis was applied to differentially expressed genes from the comparison TP3 vs. Control. The number of genes belonging to a GO term represented on the microarray (annotated), the number genes in the analyzed gene list (significant) and the expected number of genes by chance are given. The upper part of the table shows GO terms that are highly significant for under-represented genes (p-value < 0.01); the lower part indicates terms that are highly significant for over-represented genes. Calculated p-values for each category from three similar methods (classic, elim, weight) are shown. Each table is separated into three different parts representing the following ontologies: Biological Process (BP), Molecular Function (MF) and Cellular Component (CC).

Opitz et al. BMC Medical Genomics 2010 3:36   doi:10.1186/1755-8794-3-36

Open Data