The gain and loss of genes during 600 million years of vertebrate evolution

Blomme, Tine; Vandepoele, Klaas; De Bodt, Stefanie; Simillion, Cedric; Maere, Steven; Van de Peer, Yves

doi:10.1186/gb-2006-7-5-r43

Table 2 Excess of gene retention in parts of the vertebrate tree

From: The gain and loss of genes during 600 million years of vertebrate evolution

GOslim label, category, description	Organism	TPs showing significant difference	TP with highest number of duplicates	q-value
GO:0006118, BP, electron transport	HS	TP13 vs TP1	TP1	6.73E-05
	DR	TP12 vs TP10	TP10	2.50E-04
	DR	TP13 vs TP10	TP10	8.60E-06
GO:0006519, BP, amino acid and derivative metabolism	HS	TP13 vs TP1	TP1	8.69E-04
	DR	TP12 vs TP10	TP10	5.37E-04
	DR	TP13 vs TP10	TP10	1.47E-08
GO:0007165, BP, signal transduction	TN	TP13 vs TP11	TP13	5.76E-04
	XT	TP13 vs TP8	TP13	9.18E-04
	RN	TP13 vs TP2	TP13	1.44E-17
	MM	TP13 vs TP3	TP13	8.32E-19
	HS	TP13 vs TP1	TP13	2.43E-02
	DR	TP12 vs TP10	TP10	3.60E-16
	DR	TP13 vs TP10	TP10	6.40E-12
GO:0003677, MF, DNA binding	XT	TP13 vs TP8	TP13	4.38E-02
	RN	TP13 vs TP2	TP13	1.20E-08
	MM	TP13 vs TP3	TP13	1.86E-07
	DR	TP12 vs TP10	TP10	1.51E-10
	DR	TP13 vs TP10	TP10	3.99E-10
GO:0004872, MF, receptor activity	TN	TP13 vs TP11	TP13	6.34E-03
	XT	TP13 vs TP8	TP13	5.83E-03
	RN	TP13 vs TP2	TP13	2.26E-11
	MM	TP13 vs TP3	TP13	7.47E-09
	DR	TP12 vs TP10	TP10	1.01E-08
	DR	TP13 vs TP10	TP10	7.37E-05
GO:0006464, BP, protein modification	RN	TP13 vs TP2	TP13	8.16E-12
	MM	TP13 vs TP3	TP13	7.26E-07
	HS	TP13 vs TP1	TP13	2.43E-02
	DR	TP12 vs TP10	TP10	1.00E-09
	DR	TP13 vs TP10	TP10	2.63E-07
GO:0005515, MF, protein binding	TN	TP13 vs TP11	TP13	5.76E-04
	XT	TP13 vs TP8	TP13	1.01E-02
	RN	TP13 vs TP2	TP13	2.31E-12
	MM	TP13 vs TP3	TP13	3.72E-08
	DR	TP12 vs TP10	TP10	7.78E-07
	DR	TP13 vs TP10	TP10	4.01E-06
GO:0007275, BP, development	TN	TP13 vs TP11	TP13	3.71E-02
	XT	TP13 vs TP8	TP13	4.50E-02
	RN	TP13 vs TP2	TP13	7.64E-08
	MM	TP13 vs TP3	TP13	1.49E-06
	HS	TP13 vs TP1	TP13	1.88E-02
	DR	TP12 vs TP10	TP10	1.18E-06
	DR	TP13 vs TP10	TP10	1.06E-03
GO:0006350, BP, transcription	TN	TP13 vs TP11	TP13	1.97E-02
	RN	TP13 vs TP2	TP13	7.13E-11
	MM	TP13 vs TP3	TP13	3.82E-11
	DR	TP12 vs TP10	TP10	1.54E-20
	DR	TP13 vs TP10	TP10	4.11E-11
GO:0003723, MF, RNA binding	RN	TP13 vs TP2	TP2	4.71E-02
	HS	TP13 vs TP1	TP1	9.08E-03
	DR	TP12 vs TP10	TP10	9.36E-04
	DR	TP13 vs TP10	TP10	3.42E-05
GO:0006811, BP, ion transport	TN	TP13 vs TP11	TP13	1.11E-02
	XT	TP13 vs TP8	TP13	1.79E-02
	RN	TP13 vs TP2	TP13	1.23E-11
	MM	TP13 vs TP3	TP13	1.34E-06
	HS	TP13 vs TP1	TP13	3.84E-02
	DR	TP12 vs TP10	TP10	8.52E-03
	DR	TP13 vs TP10	TP10	1.00E-02

The GOslim label, its category (MF, molecular function; BP, biological process) and the general description are shown. For each organism (HS, human; MM, mouse; RN, rat; GG, chicken; XT, frog; DR, zebrafish; TN, Tetraodon), the number of species-specific duplicates was compared to the number of duplicates from time points (TPs) coinciding with WGDs (TP12 and TP13). The time points showing a significant difference (q < 0.05) in comparison are shown (TPx vs TPy), followed by the time point with the highest number of duplicates. The last column shows the q-value. Only significant results that are discussed in the text are listed (others can be found in Additional data file 1; Table S2).

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