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Table 3 GO enrichment analysis of linkage disequilibrium block on LG02

From: Highly localized divergence within supergenes in Atlantic cod (Gadus morhua) within the Gulf of Maine

GO.ID

Term

Annotated

Significant

Fisher pval

padj

GO:0006325

chromatin organization

142

18

1.70E-14

2.52E-11

GO:0065004

protein-DNA complex assembly

105

16

2.80E-14

2.52E-11

GO:0071824

protein-DNA complex subunit organization

105

16

2.80E-14

2.52E-11

GO:0051276

chromosome organization

178

19

7.10E-14

4.76E-11

GO:0006334

nucleosome assembly

100

15

2.50E-13

9.39E-11

GO:0031497

chromatin assembly

100

15

2.50E-13

9.39E-11

GO:0034728

nucleosome organization

100

15

2.50E-13

9.39E-11

GO:0006333

chromatin assembly or disassembly

101

15

2.90E-13

9.57E-11

GO:0006323

DNA packaging

106

15

6.00E-13

1.77E-10

GO:0071103

DNA conformation change

112

15

1.40E-12

3.65E-10

GO:0034622

cellular macromolecular complex assembly

180

16

1.30E-10

3.26E-08

GO:0043933

macromolecular complex subunit organization

324

20

3.90E-10

8.64E-08

GO:0006461

protein complex assembly

244

17

1.50E-09

2.91E-07

GO:0070271

protein complex biogenesis

244

17

1.50E-09

2.91E-07

GO:0065003

macromolecular complex assembly

258

17

3.60E-09

6.38E-07

GO:0071822

protein complex subunit organization

271

17

7.50E-09

1.24E-06

GO:0022607

cellular component assembly

308

18

7.90E-09

1.24E-06

GO:0006996

organelle organization

432

21

1.00E-08

1.50E-06

GO:0044085

cellular component biogenesis

339

18

3.50E-08

4.95E-06

GO:0016043

cellular component organization

636

22

1.70E-06

0.00023

GO:0071840

cellular component organization or biogenesis

666

22

3.70E-06

0.00047

GO:0042157

lipoprotein metabolic process

32

5

2.70E-05

0.0032

GO:0044711

single-organism biosynthetic-process

295

9

0.0061

0.7060

GO:0006897

endocytosis

35

3

0.0071

0.7895

GO:0043543

protein acylation

12

2

0.0078

0.8318

GO:0016568

chromatin modification

38

3

0.0089

0.8645

  1. Using topGO, (in R), enrichment analysis shows multiple GO categories that may be enriched in the LD block from LG02, mostly centered on DNA/chromatin structuring. Total number of annotated genes in each GO category is shown, as well as those within the LD block that are significant (Fisher test p < 0.01). Multiple-test correction (calculated as false-discovery rate, ‘fdr’) is shown in p-adj column, p-values < 0.05 shown in bold