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Table 4 Domains present in lineages under positive selection

From: Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates

Over-Represented CATH Domain Topologies in TAED

CATH domain topology

Mapped Lineages Under Positive Selection

Lineages Under Positive Selection Mapped

Uncorrected P-value

FDR P-value

Bonferroni P-value

Rossmann fold

7.35%

25.55%

<  0.0001

<  0.0001

<  0.0001

Jelly Rolls

7.30%

4.43%

<  0.0001

<  0.0001

0.0013

Phosphorylase Kinase domain 1

9.51%

3.87%

<  0.0001

<  0.0001

<  0.0001

TIM Barrel

7.52%

3.59%

<  0.0001

<  0.0001

<  0.0001

Thrombin subunit H

11.13%

2.90%

<  0.0001

<  0.0001

<  0.0001

Ubiquitin-like (UB roll)

7.06%

2.50%

0.0143

0.0355

1.0000

Glutaredoxin

9.53%

2.39%

<  0.0001

<  0.0001

<  0.0001

Collagenase (Catalytic Domain)

9.70%

2.22%

<  0.0001

<  0.0001

<  0.0001

DNA polymerase domain 1

8.26%

2.12%

<  0.0001

<  0.0001

<  0.0001

OB fold (Dihydrolipoamide Acetyltransferase E2P)

7.32%

1.79%

0.0013

0.0039

0.8113

Methane Monooxygenase Hydroxylase Chain G domain 1

8.24%

1.55%

<  0.0001

<  0.0001

<  0.0001

Cytochrome p450

9.11%

1.51%

<  0.0001

<  0.0001

<  0.0001

Helicase Ruva Protein domain 3

9.86%

1.21%

<  0.0001

<  0.0001

<  0.0001

Laminin

8.56%

1.03%

<  0.0001

<  0.0001

<  0.0001

Glutathione S-transferase Yfyf (Class Pi) Chain A domain 2

10.79%

1.01%

<  0.0001

<  0.0001

<  0.0001

Kinesin

8.47%

1.00%

<  0.0001

<  0.0001

<  0.0001

Glycosyltransferase

12.75%

0.92%

<  0.0001

<  0.0001

<  0.0001

FAD/NAD(P)-binding domain

10.68%

0.87%

<  0.0001

<  0.0001

<  0.0001

2-enoyl-CoA Hydratase Chain A domain 1

14.07%

0.80%

<  0.0001

<  0.0001

<  0.0001

Erythroid Transcription Factor GATA-1 Chain A

9.34%

0.72%

<  0.0001

<  0.0001

<  0.0001

Cyclin A domain 1

10.32%

0.71%

<  0.0001

<  0.0001

<  0.0001

Alkaline Phosphatase subunit A

9.96%

0.69%

<  0.0001

<  0.0001

<  0.0001

Butyryl-CoA Dehydrogenase subunit A domain 3

9.13%

0.68%

<  0.0001

<  0.0001

<  0.0001

Carbonic Anhydrase II

14.52%

0.66%

<  0.0001

<  0.0001

<  0.0001

  1. Enrichment analysis of CATH domain topologies in TAED showing CATH domains topologies present in highest % of lineages under positive selection. All pathways were significant at the 0.05 level after correction with the false discovery rate (FDR). Bold numbers indicate not significant at the 0.05 level. Lineages with dN/dS > 1 considered under positive selection