GO term	gene number	Medaka-SN-KaKs	gene number	human-chimp-KaKs	GO number
bone remodeling	11	0.201954397	25	0.322830773	GO:0046849
response to bacteria	13	0.192	35	0.304876977	GO:0009617
sex differentiation	14	0.24764278	11	0.375061065	GO:0007548
DNA replication initiation	11	0.14416476	17	0.199157755	GO:0006270
regulation of immune response	10	0.290951178	10	0.398131626	GO:0050776
humoral immune response	26	0.238921958	119	0.326612064	GO:0006959
transition metal ion transport	14	0.212234433	28	0.282072217	GO:0000041
male gamete generation	40	0.272355843	80	0.354436307	GO:0048232
positive regulation of metabolism	23	0.210300429	22	0.272393684	GO:0009893
humoral defense mechanism (sensu Vertebrata)	18	0.253808978	88	0.320903301	GO:0016064
activation of MAPK	20	0.163325048	14	0.205467252	GO:0000187
cellular defense response	18	0.269713904	59	0.338665683	GO:0006968
L-amino acid transport	11	0.162601626	10	0.203798981	GO:0015807
amine catabolism	27	0.225519288	33	0.276076231	GO:0009310
gametogenesis	54	0.274661509	98	0.335056327	GO:0007276
reproduction	68	0.284639336	118	0.344178048	GO:0000003
response to xenobiotic stimulus	11	0.326139089	43	0.383463079	GO:0009410
regulation of biosynthesis	28	0.219202438	49	0.255368697	GO:0009889
membrane fusion	13	0.363057325	17	0.422535025	GO:0006944
hemopoiesis	25	0.215469613	56	0.247451367	GO:0030097
organic acid biosynthesis	27	0.18707483	35	0.199639162	GO:0016053
cell activation	21	0.257575758	69	0.272268619	GO:0001775
fertilization	14	0.345776281	25	0.36498265	GO:0009566
lymphocyte differentiation	10	0.17999531	27	0.187498377	GO:0030098
regulation of metabolism	194	0.238649941	65	0.247051405	GO:0019222
phagocytosis	11	0.183486239	19	0.189207117	GO:0006909
digestion	31	0.284416492	35	0.290332458	GO:0007586
antimicrobial humoral response	15	0.28440367	71	0.29009536	GO:0019730
positive regulation of transcription	16	0.196335625	35	0.19852784	GO:0045941
coagulation	51	0.307692308	60	0.304400554	GO:0050817
translational elongation	14	0.225128774	13	0.221956684	GO:0006414
meiosis I	12	0.252902805	16	0.248803793	GO:0007127
metal ion homeostasis	32	0.220972981	42	0.217325332	GO:0006875
pregnancy	20	0.395035792	34	0.384283456	GO:0007565
immune response	189	0.335978836	534	0.323979109	GO:0006955
hemostasis	54	0.303099886	61	0.291890125	GO:0007599
homophilic cell adhesion	66	0.254129129	101	0.24411674	GO:0007156
response to endogenous stimulus	109	0.275132275	158	0.263827738	GO:0009719
inflammatory response	58	0.29709314	155	0.28268124	GO:0006954
response to wounding	126	0.292537314	212	0.277444001	GO:0009611
reproductive physiological process	22	0.395035792	41	0.370811333	GO:0050876
response to biotic stimulus	258	0.331625782	650	0.309817599	GO:0009607
positive regulation of programmed cell death	51	0.242165242	94	0.225646792	GO:0043068
defense response	203	0.350931677	593	0.324703762	GO:0006952
steroid metabolism	72	0.216833281	94	0.200374988	GO:0008202
response to external stimulus	404	0.311273009	1001	0.283655907	GO:0009605
response to stress	345	0.294294294	594	0.266338136	GO:0006950
regulation of physiological process	489	0.266791045	57	0.24104373	GO:0050791
DNA replication	73	0.252380952	102	0.227847131	GO:0006260
regulation of blood pressure	17	0.303921569	28	0.274363217	GO:0008217
regulation of programmed cell death	91	0.254237288	95	0.228084619	GO:0043067
glutamine family amino acid metabolism	22	0.208608059	29	0.186996336	GO:0009064
regulation of body fluids	64	0.311692249	71	0.278390007	GO:0050878
steroid biosynthesis	23	0.204359673	45	0.182511713	GO:0006694
negative regulation of metabolism	45	0.210300429	19	0.187533292	GO:0009892
transition metal ion homeostasis	14	0.313931951	16	0.279858779	GO:0046916
DNA recombination	34	0.280469083	45	0.24992625	GO:0006310
cell cycle checkpoint	15	0.403409091	27	0.354289799	GO:0000075
response to stimulus	664	0.315367988	1184	0.276734231	GO:0050896
sensory perception of light	117	0.246537396	104	0.215518804	GO:0050953
pattern specification	10	0.17208762	16	0.149489862	GO:0007389
DNA repair	93	0.297491039	121	0.258101912	GO:0006281
aromatic compound metabolism	32	0.294124634	55	0.253576512	GO:0006725
calcium ion homeostasis	16	0.19914399	22	0.171633284	GO:0006874
regulation of cyclin dependent protein kinase activity	15	0.25	33	0.213521397	GO:0000079
organismal physiological process	680	0.310999445	1145	0.262091815	GO:0050874
viral infectious cycle	11	0.259493671	24	0.216333994	GO:0019058
detection of external stimulus	181	0.313901345	251	0.260758018	GO:0009581
hormone metabolism	22	0.285726765	25	0.234712039	GO:0042445
cell cycle arrest	28	0.294783779	43	0.239456932	GO:0007050
response to drug	15	0.392226148	17	0.318067561	GO:0042493
lipid transport	30	0.293798027	44	0.237900795	GO:0006869
excretion	21	0.312101911	33	0.25150945	GO:0007588
sensory perception	175	0.313901345	223	0.252907528	GO:0007600
amino acid metabolism	115	0.260869565	138	0.207729305	GO:0006520
regulation of cell growth	41	0.272058824	70	0.21628408	GO:0001558
regulation of transcription	152	0.238649941	1170	0.186040607	GO:0045449
serine family amino acid metabolism	13	0.279069767	17	0.214686869	GO:0009069
amino acid and derivative metabolism	131	0.273469388	162	0.210247322	GO:0006519
taxis	22	0.341165815	98	0.262261884	GO:0042330
organic acid metabolism	209	0.264094955	256	0.202205299	GO:0006082
sterol biosynthesis	13	0.188908146	19	0.144287569	GO:0016126
death	217	0.30749354	344	0.234460869	GO:0016265
response to radiation	23	0.310580205	29	0.236241309	GO:0009314
regulation of cellular process	536	0.281517439	430	0.213212989	GO:0050794
cyclic nucleotide metabolism	22	0.262921909	25	0.197211972	GO:0009187
cell death	214	0.306153187	342	0.229568306	GO:0008219
tRNA processing	21	0.290322581	26	0.217466387	GO:0008033
embryonic development	17	0.213740458	39	0.159430114	GO:0009790
programmed cell death	198	0.311886305	323	0.231048145	GO:0012501
cell adhesion	331	0.316708229	429	0.234106951	GO:0007155
lipid catabolism	43	0.305555556	50	0.225712446	GO:0016042
cell cycle	319	0.257217848	510	0.188993249	GO:0007049
amino acid transport	38	0.237675317	41	0.174174384	GO:0006865
proteolysis and peptidolysis	235	0.314984709	390	0.230456887	GO:0006508
ribosome biogenesis and assembly	23	0.29342723	23	0.214127631	GO:0042254
nucleocytoplasmic transport	35	0.258461538	63	0.188307267	GO:0006913
catabolism	393	0.302788845	585	0.220443338	GO:0009056
organic anion transport	13	0.264957265	26	0.191918244	GO:0015711
M phase	105	0.252380952	118	0.182673613	GO:0000279
protein catabolism	239	0.314984709	401	0.227669892	GO:0030163
fatty acid metabolism	78	0.275786614	87	0.199278629	GO:0006631
growth	68	0.279562535	32	0.201526894	GO:0040007
sterol metabolism	44	0.216478295	44	0.156043731	GO:0016125
organelle organization and biogenesis	256	0.256323881	227	0.184274344	GO:0006996
lipoprotein metabolism	13	0.283928571	19	0.203609211	GO:0042157
macromolecule catabolism	286	0.313589445	422	0.224452564	GO:0009057
microtubule cytoskeleton organization and biogenesis	22	0.260600031	31	0.185960925	GO:0000226
response to chemical substance	68	0.379822897	186	0.268093621	GO:0042221
DNA metabolism	242	0.283177438	372	0.199459652	GO:0006259
organic acid transport	56	0.249974648	55	0.173580402	GO:0015849
cell differentiation	152	0.306585062	145	0.212502251	GO:0030154
circulation	46	0.307670127	80	0.212458486	GO:0008015
negative regulation of apoptosis	31	0.301886792	78	0.207829151	GO:0043066
amine metabolism	157	0.287671233	197	0.197783657	GO:0009308
I-kappaB kinase/NF-kappaB cascade	46	0.313306569	91	0.214366497	GO:0007249
regulation of protein biosynthesis	26	0.240218041	24	0.163319497	GO:0006417
rRNA metabolism	15	0.4	22	0.271367533	GO:0016072
protein complex assembly	84	0.273844365	70	0.185710537	GO:0006461
mitochondrial transport	14	0.187668245	16	0.127229905	GO:0006839
nucleoside metabolism	12	0.380067056	18	0.257172514	GO:0009116
protein folding	97	0.251141553	95	0.16906959	GO:0006457
cell proliferation	108	0.295443831	760	0.198657786	GO:0008283
metabolism	2537	0.287066246	4365	0.192337103	GO:0008152
regulation of protein kinase activity	42	0.261029412	42	0.174882665	GO:0045859
striated muscle contraction	29	0.189873418	18	0.127020134	GO:0006941
cytoskeleton organization and biogenesis	120	0.257270851	173	0.171965379	GO:0007010
transcription	478	0.276708685	1238	0.184230406	GO:0006350
protein secretion	10	0.297902369	22	0.19810504	GO:0009306
one-carbon compound metabolism	20	0.30568789	23	0.20218925	GO:0006730
negative regulation of transcription	39	0.210300429	90	0.138980498	GO:0016481
nucleotide metabolism	72	0.298340482	113	0.19631445	GO:0009117
cytoplasm organization and biogenesis	32	0.282181596	256	0.184752374	GO:0007028
RNA localization	12	0.223593952	15	0.146247093	GO:0006403
nucleic acid transport	12	0.223593952	15	0.146247093	GO:0050657
regulation of cell size	56	0.292480862	94	0.190704375	GO:0008361
cellular physiological process	3657	0.292372881	2814	0.190508423	GO:0050875
protein biosynthesis	192	0.282140624	371	0.183055255	GO:0006412
JAK-STAT cascade	18	0.219601156	25	0.142408964	GO:0007259
protein metabolism	956	0.283950617	1643	0.18403816	GO:0019538
electron transport	145	0.351351351	216	0.227157982	GO:0006118
cell organization and biogenesis	324	0.260925478	511	0.168502768	GO:0016043
translation	65	0.273049645	112	0.175975626	GO:0043037
angiogenesis	23	0.312977099	36	0.20157628	GO:0001525
energy reserve metabolism	25	0.214634146	14	0.137942724	GO:0006112
lipid metabolism	288	0.29247715	371	0.187956045	GO:0006629
positive regulation of signal transduction	47	0.31641791	69	0.202683881	GO:0009967
ribonucleotide metabolism	22	0.33710711	49	0.214949188	GO:0009259
regulation of cell cycle	168	0.285508432	296	0.181803339	GO:0000074
cell communication	1375	0.309608541	2297	0.196771115	GO:0007154
cellular morphogenesis	79	0.28440367	121	0.180608868	GO:0000902
G-protein coupled receptor protein signaling pathway	220	0.336290072	494	0.213247999	GO:0007186
cAMP metabolism	14	0.23690441	12	0.14975874	GO:0046058
histogenesis	60	0.297491616	65	0.18594521	GO:0009888
ion homeostasis	45	0.248878924	57	0.154752883	GO:0050801
ectoderm development	23	0.328571429	43	0.204223724	GO:0007398
heterocycle metabolism	27	0.333333333	32	0.207134469	GO:0046483
mitotic cell cycle	105	0.25	145	0.154922825	GO:0000278
endocytosis	92	0.288636637	88	0.178785278	GO:0006897
blood vessel development	25	0.327272727	36	0.20157628	GO:0001568
cytokinesis	89	0.287179487	67	0.175279314	GO:0000910
tRNA metabolism	43	0.350364964	52	0.213488285	GO:0006399
ER to Golgi transport	19	0.322580645	19	0.195649873	GO:0006888
macromolecule biosynthesis	227	0.287066246	606	0.173749758	GO:0009059
carbohydrate metabolism	209	0.26744186	253	0.16168269	GO:0005975
amino acid derivative metabolism	20	0.366909091	32	0.221731444	GO:0006575
protein kinase cascade	129	0.301282051	187	0.18172398	GO:0007243
coenzyme metabolism	35	0.248175182	76	0.14954875	GO:0006732
signal transduction	995	0.309782609	1827	0.1864349	GO:0007165
meiosis	23	0.253424658	29	0.152475393	GO:0007126
response to abiotic stimulus	154	0.367813967	294	0.22114287	GO:0009628
transport	1058	0.295798742	1213	0.177541523	GO:0006810
sphingoid metabolism	11	0.283333333	14	0.169429235	GO:0046519
biosynthesis	419	0.290836653	718	0.173743088	GO:0009058
protein amino acid phosphorylation	11	0.247787611	408	0.14801752	GO:0006468
intracellular transport	262	0.27634885	378	0.164516299	GO:0046907
intra-Golgi transport	16	0.31261062	11	0.18590499	GO:0006891
homeostasis	52	0.291811687	77	0.173241776	GO:0042592
regulation of cell adhesion	11	0.287066246	19	0.168707621	GO:0030155
cell surface receptor linked signal transduction	376	0.330721864	808	0.19421282	GO:0007166
inorganic anion transport	74	0.379541735	47	0.221311949	GO:0015698
RNA modification	29	0.290322581	38	0.168610646	GO:0009451
nucleotide biosynthesis	48	0.337611598	81	0.195505561	GO:0009165
skeletal development	68	0.356017806	95	0.205649326	GO:0001501
cell homeostasis	48	0.272238204	67	0.156615844	GO:0019725
lipid biosynthesis	80	0.261462944	128	0.149848876	GO:0008610
response to light	14	0.483861531	17	0.275844907	GO:0009416
RNA metabolism	156	0.292900056	248	0.166880032	GO:0016070
regulation of translation	21	0.212598425	54	0.121057552	GO:0006445
regulation of signal transduction	74	0.316705687	112	0.180106776	GO:0009966
glycolipid metabolism	11	0.260299625	19	0.147506417	GO:0006664
protein modification	390	0.283939594	772	0.160325474	GO:0006464
M phase of mitotic cell cycle	84	0.260289171	91	0.146428032	GO:0000087
icosanoid metabolism	13	0.331491713	22	0.186405289	GO:0006690
neurophysiological process	284	0.343771405	413	0.192979167	GO:0050877
muscle contraction	79	0.234567901	85	0.131540799	GO:0006936
amino acid activation	24	0.35123882	27	0.195290142	GO:0043038
sphingolipid metabolism	22	0.282843137	35	0.157251602	GO:0006665
protein transport	262	0.312391087	295	0.173295273	GO:0015031
anion transport	97	0.363636364	84	0.201696958	GO:0006820
neuropeptide signaling pathway	28	0.351844958	71	0.195032729	GO:0007218
transforming growth factor beta receptor signaling pathway	12	0.259336843	22	0.143647814	GO:0007179
extracellular structure organization and biogenesis	18	0.365593017	23	0.202494026	GO:0043062
chloride transport	24	0.285368955	27	0.15758721	GO:0006821
transmembrane receptor protein serine/threonine kinase signaling pathway	20	0.259336843	28	0.142870193	GO:0007178
protein targeting	47	0.364764268	96	0.20002197	GO:0006605
intracellular protein transport	158	0.303846154	283	0.166061335	GO:0006886
phosphorylation	28	0.269364465	460	0.147164067	GO:0016310
RNA processing	121	0.290322581	197	0.158492897	GO:0006396
morphogenesis	531	0.301829268	803	0.164377513	GO:0009653
amino acid biosynthesis	27	0.247159091	29	0.13449514	GO:0008652
alcohol biosynthesis	15	0.263929619	16	0.140883716	GO:0046165
tRNA modification	27	0.350364964	31	0.186421155	GO:0006400
cation transport	212	0.263419743	304	0.139002243	GO:0006812
glutamine metabolism	15	0.20952381	13	0.109377172	GO:0006541
secretion	92	0.308008193	53	0.160260001	GO:0046903
organogenesis	415	0.30952381	641	0.161034841	GO:0009887
muscle development	81	0.259036145	79	0.134382158	GO:0007517
purine nucleotide metabolism	25	0.336283186	48	0.174368559	GO:0006163
intracellular signaling cascade	393	0.310195228	688	0.160573376	GO:0007242
membrane lipid metabolism	48	0.282843137	88	0.146363696	GO:0006643
alcohol metabolism	124	0.295707344	142	0.152995823	GO:0006066
regulation of enzyme activity	79	0.272727273	59	0.140931413	GO:0050790
response to toxin	10	0.400902771	11	0.206941082	GO:0009636
tricarboxylic acid cycle	14	0.144544582	15	0.074560659	GO:0006099
cell motility	121	0.303921569	209	0.156381792	GO:0006928
Golgi vesicle transport	40	0.310326087	45	0.158252128	GO:0048193
energy derivation by oxidation of organic compounds	84	0.251490511	76	0.128162113	GO:0015980
ion transport	331	0.302238806	434	0.153377449	GO:0006811
mRNA metabolism	46	0.207688102	113	0.104532643	GO:0016071
amine biosynthesis	38	0.311805872	44	0.156346149	GO:0009309
aminoglycan metabolism	23	0.3514377	22	0.1747326	GO:0006022
monosaccharide metabolism	59	0.269896194	74	0.133957173	GO:0005996
metal ion transport	169	0.261455526	229	0.128220512	GO:0030001
cell migration	48	0.311965582	37	0.150170283	GO:0016477
phosphorus metabolism	55	0.318681319	563	0.152064783	GO:0006793
mesoderm development	12	0.290296496	20	0.138138978	GO:0007498
second-messenger-mediated signaling	73	0.311418685	90	0.148122733	GO:0019932
polysaccharide metabolism	27	0.26744186	24	0.127164025	GO:0005976
heart development	16	0.274566547	17	0.13009002	GO:0007507
sodium ion transport	54	0.23973293	54	0.113	GO:0006814
receptor mediated endocytosis	14	0.340164056	17	0.159407915	GO:0006898
main pathways of carbohydrate metabolism	51	0.248175182	55	0.115891714	GO:0006092
secretory pathway	67	0.278317152	93	0.129058811	GO:0045045
pigment metabolism	15	0.470779221	17	0.218193069	GO:0042440
detection of abiotic stimulus	72	0.367680878	84	0.169631889	GO:0009582
regulation of G-protein coupled receptor protein signaling pathway	20	0.340242165	20	0.155366121	GO:0008277
phospholipid metabolism	29	0.283928571	53	0.129269807	GO:0006644
DNA packaging	75	0.262987013	141	0.119693005	GO:0006323
hydrogen transport	25	0.211981567	48	0.094251876	GO:0006818
calcium ion transport	38	0.223521764	41	0.099137986	GO:0006816
sulfur amino acid metabolism	14	0.368289417	16	0.160844112	GO:0000096
glucose metabolism	46	0.280366423	51	0.122429938	GO:0006006
sulfur metabolism	22	0.335217058	37	0.145050067	GO:0006790
glycolysis	22	0.253346188	26	0.109319473	GO:0006096
neurogenesis	173	0.312977099	292	0.133868369	GO:0007399
chromatin modification	59	0.27734375	58	0.118575404	GO:0016568
monovalent inorganic cation transport	143	0.261455526	195	0.111333566	GO:0015672
membrane lipid biosynthesis	16	0.256465602	47	0.109043857	GO:0046467
RNA splicing	33	0.306666667	87	0.130129555	GO:0008380
carbohydrate transport	13	0.355263158	21	0.150493174	GO:0008643
amino acid derivative biosynthesis	12	0.511033734	17	0.216352908	GO:0042398
exocytosis	20	0.241890441	39	0.102299112	GO:0006887
axon guidance	22	0.311184682	14	0.1299908	GO:0007411
neurotransmitter transport	30	0.344832299	22	0.142035609	GO:0006836
alcohol catabolism	30	0.298584461	38	0.122687283	GO:0046164
porphyrin metabolism	17	0.385714286	14	0.158322354	GO:0006778
enzyme linked receptor protein signaling pathway	72	0.341927018	117	0.140063357	GO:0007167
glycoprotein metabolism	39	0.422382671	102	0.171385679	GO:0009100
central nervous system development	21	0.38547486	76	0.154956777	GO:0007417
vitamin metabolism	21	0.370558376	26	0.146403983	GO:0006766
oxygen and reactive oxygen species metabolism	30	0.412589134	42	0.162873832	GO:0006800
histone modification	13	0.403773585	10	0.159035376	GO:0016570
glycerophospholipid metabolism	12	0.268280075	22	0.105493263	GO:0006650
ubiquitin cycle	256	0.265734589	70	0.104303706	GO:0006512
sensory perception of mechanical stimulus	53	0.368539326	57	0.142675009	GO:0050954
detection of mechanical stimulus	54	0.369875724	57	0.142675009	GO:0050982
dephosphorylation	13	0.470873786	98	0.178743463	GO:0016311
glucan metabolism	20	0.239078073	11	0.089446178	GO:0006073
transmission of nerve impulse	118	0.369453389	198	0.137776581	GO:0019226
chromosome segregation	28	0.207720888	11	0.076822648	GO:0007059
response to oxidative stress	24	0.439560583	27	0.161851554	GO:0006979
small GTPase mediated signal transduction	22	0.333992808	169	0.120742268	GO:0007264
Wnt receptor signaling pathway	39	0.263736264	68	0.095292144	GO:0016055
transmembrane receptor protein tyrosine kinase signaling pathway	44	0.36882938	79	0.132271146	GO:0007169
carbohydrate biosynthesis	38	0.370875223	59	0.131359303	GO:0016051
glycerol ether metabolism	10	0.356916506	16	0.126278297	GO:0006662
glycerolipid metabolism	10	0.356916506	16	0.126278297	GO:0046486
neutral lipid metabolism	10	0.356916506	16	0.126278297	GO:0006638
potassium ion transport	80	0.297052473	114	0.104655754	GO:0006813
DNA modification	19	0.284722222	14	0.100255124	GO:0006304
axonogenesis	30	0.319109909	19	0.111233841	GO:0007409
fatty acid oxidation	13	0.533519553	17	0.181864741	GO:0019395
regulation of neurotransmitter levels	21	0.351758794	33	0.11821122	GO:0001505
JNK cascade	20	0.348288924	23	0.115422575	GO:0007254
protein kinase C activation	15	0.314285714	17	0.103497514	GO:0007205
regulation of mitosis	15	0.482517483	27	0.15823472	GO:0007088
nucleoside triphosphate metabolism	12	0.394398576	39	0.124392647	GO:0009141
actin cytoskeleton organization and biogenesis	18	0.451755882	60	0.12606739	GO:0030036
monovalent inorganic cation homeostasis	11	0.248878924	12	0.068115002	GO:0030004
negative regulation of enzyme activity	11	0.301775148	21	0.080996595	GO:0043086
frizzled signaling pathway	13	0.188	13	0.049108433	GO:0007222
learning and/or memory	11	0.452054795	15	0.117365629	GO:0007611
transcription initiation	25	0.341463415	34	0.08692016	GO:0006352
myogenesis	11	0.407665505	15	0.09773933	GO:0007519
regulation of adenylate cyclase activity	14	0.335761524	11	0.075308697	GO:0045761