Table 2 Top 20 over and underrepresented GO terms in the list of Peromyscus genes containing a nonsynonymous SNP between P. maniculatus and P. polionotus

Overrepresented GO terms

GO term ID

p-value

Number of Mus genes with GO term

Expected number of genes

Number of Peromyscus Genes with non-synonymous SNP

cellular process

GO:0009987

2.03E-298

15,748

6516

7781

cellular metabolic process

GO:0044237

8.06E-257

9331

3861

5119

metabolic process

GO:0008152

2.96E-243

10,435

4318

5557

primary metabolic process

GO:0044238

5.83E-235

9405

3891

5096

organic substance metabolic process

GO:0071704

8.98E-225

9966

4124

5310

nitrogen compound metabolic process

GO:0006807

2.89E-214

8892

3679

4819

cellular component organization or biogenesis

GO:0071840

5.56E-214

6225

2576

3618

cellular component organization

GO:0016043

9.53E-201

6053

2505

3505

localization

GO:0051179

3.18E-193

5918

2449

3423

cellular macromolecule metabolic process

GO:0044260

2.50E-174

7080

2929

3905

macromolecule metabolic process

GO:0043170

3.99E-170

8461

3501

4506

organonitrogen compound metabolic process

GO:1901564

9.62E-137

6215

2572

3402

developmental process

GO:0032502

4.23E-136

6193

2562

3390

anatomical structure development

GO:0048856

1.40E-130

5810

2404

3198

establishment of localization

GO:0051234

1.11E-127

4518

1869

2588

biological regulation

GO:0065007

1.61E-120

12,092

5003

5874

multicellular organism development

GO:0007275

1.36E-119

5304

2195

2931

transport

GO:0006810

4.07E-118

4378

1811

2494

organelle organization

GO:0006996

2.00E-117

3549

1468

2095

macromolecule modification

GO:0043412

7.62E-114

3623

1499

2121

Underrepresented GO terms

GO term ID

p-value

Number of Mus genes with GO term

Expected number of genes

Number of BW Genes with non-synonymous SNP

sensory perception of smell

GO:0007608

3.37E-238

1138

471

17

sensory perception of chemical stimulus

GO:0007606

2.58E-228

1236

511

39

sensory perception

GO:0007600

1.17E-116

1784

738

303

G protein-coupled receptor signaling pathway

GO:0007186

2.04E-83

1921

795

410

nervous system process

GO:0050877

8.09E-55

2286

946

606

system process

GO:0003008

2.91E-25

2923

1209

955

phagocytosis, recognition

GO:0006910

3.11E-23

151

62

9

response to pheromone

GO:0019236

1.07E-21

105

43

2

complement activation, classical pathway

GO:0006958

1.28E-19

165

68

16

humoral immune response mediated by circulating immunoglobulin

GO:0002455

3.89E-17

180

74

23

complement activation

GO:0006956

1.02E-15

187

77

27

humoral immune response

GO:0006959

6.06E-15

355

147

78

phagocytosis, engulfment

GO:0006911

4.56E-12

189

78

34

protein activation cascade

GO:0072376

1.11E-11

200

83

38

B cell receptor signaling pathway

GO:0050853

2.16E-11

181

75

33

xenobiotic metabolic process

GO:0006805

2.19E-11

112

46

14

plasma membrane invagination

GO:0099024

6.36E-11

198

82

39

membrane invagination

GO:0010324

1.60E-10

205

85

42

response to leukemia inhibitory factor

GO:1990823

1.06E-09

311

129

78

cellular response to leukemia inhibitory factor

GO:1990830

1.06E-09

311

129

78