Table 2.

GO term enrichment of protein families died at the ancestor of free-living nematodes and not present in the outgroup species.

GO Category	GO term	GO descriptor	Under-represent P value	Over-represent P value
Biological processes
	GO:0006139	nucleobase, nucleoside, nucleotide and na metabolic process	0.137	1.000
	GO:0006260	DNA replication	0.977	0.215
	GO:0006281	DNA repair	0.964	0.265
	GO:0006351	transcription, DNA-dependent	0.409	0.872
	GO:0006352	transcription initiation	1.000	0.006
	GO:0006397	mRNA processing	0.998	0.065
	GO:0006450	regulation of translational fidelity	1.000	0.002
	GO:0006461	protein complex assembly	0.996	0.092
	GO:0006508	proteolysis	0.933	0.249
	GO:0006511	ubiquitin-dependent protein catabolic process	0.983	0.186
	GO:0006810	transport	0.249	1.000
	GO:0006811	ion transport	0.439	1.000
	GO:0006886	intracellular protein transport	0.967	0.251
	GO:0007049	cell cycle	0.988	0.154
	GO:0007154	cell communication	0.292	1.000
	GO:0007186	G-protein coupled receptor protein signaling pathway	0.900	0.424
	GO:0008152	metabolic process	0.193	1.000
	GO:0008154	actin polymerization and/or depolymerization	1.000	0.016
	GO:0009058	biosynthetic process	0.395	1.000
	GO:0009439	cyanate metabolic process	1.000	0.004
	GO:0009987	cellular process	0.131	0.975
	GO:0016192	vesicle-mediated transport	0.987	0.160
	GO:0016998	cell wall catabolic process	0.999	0.041
	GO:0032259	methylation	0.990	0.143
	GO:0043283	biopolymer metabolic process	0.204	0.953
	GO:0044238	primary metabolic process	0.326	0.874
	GO:0044249	cellular biosynthetic process	0.179	1.000
	GO:0050794	regulation of cellular process	0.096	0.983
Molecular function
	GO:0000166	nucleotide binding	0.924	0.217
	GO:0003676	nucleic acid binding	0.847	0.262
	GO:0003700	transcription factor activity	0.462	0.780
	GO:0003735	structural constituent of ribosome	0.424	1.000
	GO:0003824	catalytic activity	0.137	1.000
	GO:0003896	DNA primase activity	1.000	0.016
	GO:0004175	endopeptidase activity	0.452	1.000
	GO:0004252	serine-type endopeptidase activity	0.941	0.328
	GO:0004298	threonine endopeptidase activity	0.999	0.036
	GO:0004871	signal transducer activity	0.151	1.000
	GO:0005083	small GTPase regulator activity	0.941	0.328
	GO:0005179	hormone activity	0.885	0.444
	GO:0005198	structural molecule activity	0.962	0.169
	GO:0005215	transporter activity	0.384	1.000
	GO:0005509	calcium ion binding	0.407	1.000
	GO:0005515	protein binding	0.996	0.010
	GO:0005524	ATP binding	0.178	0.959
	GO:0008073	ornithine decarboxylase inhibitor activity	1.000	0.020
	GO:0008158	hedgehog receptor activity	0.999	0.048
	GO:0008234	cysteine-type peptidase activity	0.899	0.420
	GO:0008270	zinc ion binding	0.957	0.089
	GO:0008324	cation transmembrane transporter activity	0.321	1.000
	GO:0008824	cyanate hydratase activity	1.000	0.007
	GO:0009055	electron carrier activity	0.450	1.000
	GO:0016301	kinase activity	0.477	0.831
	GO:0016491	oxidoreductase activity	0.061	1.000
	GO:0016740	transferase activity	0.198	0.952
	GO:0016787	hydrolase activity	0.428	0.857
	GO:0016788	hydrolase activity, acting on ester bonds	0.262	1.000
	GO:0016836	hydro-lyase activity	0.996	0.094
	GO:0016874	ligase activity	0.483	1.000
	GO:0016986	transcription initiation factor activity	1.000	0.003
	GO:0017111	nucleoside-triphosphatase activity	0.437	1.000
	GO:0022857	transmembrane transporter activity	0.498	1.000
	GO:0022892	substrate-specific transporter activity	0.414	1.000
	GO:0030234	enzyme regulator activity	0.386	1.000
	GO:0030528	transcription regulator activity	0.312	1.000
	GO:0042578	phosphoric ester hydrolase activity	0.489	1.000
	GO:0043169	cation binding	0.459	1.000
	GO:0043565	sequence-specific DNA binding	0.150	1.000
	GO:0046872	metal ion binding	0.320	1.000
	GO:0046983	protein dimerization activity	0.901	0.416
	GO:0048037	cofactor binding	0.427	1.000
	GO:0051537	2 iron, 2 sulfur cluster binding	1.000	0.032