Table 2.

Gene ontologies (GO) of GUPS (105 for E. siliculosus, 110 for S. japonica).

Ontology	GO ID	Term	No. of genes (Es:Sj)	Percentage of gene No. (Es:Sj)
CC	GO:0005623	cell	40:49	38.1:44.5*
	GO:0019012	virion	1:0	1.0:0.0
	GO:0031974	membrane-enclosed lumen	2:1	1.9:0.9
	GO:0031975	envelope	1:0	1.0:0.0
	GO:0032991	macromolecular complex	9:12	8.6:10.9
	GO:0043226	organelle	11:19	10.5:17.3
	GO:0055044	symplast	1:0	1.0:0.0
MF	GO:0003824	catalytic activity	38:46	36.2:41.8
	GO:0005198	structural molecule activity	1:2	1.0:1.8
	GO:0005215	transporter activity	3:6	2.9:5.5
	GO:0005488	binding	36:36	34.3:32.7
	GO:0030234	enzyme regulator activity	0:2	0.0:1.8
	GO:0030528	transcription regulator activity	0:1	0.0:0.9
	GO:0045182	translation regulator activity	2:1	1.9:0.9
	GO:0060089	molecular transducer activity	1:0	1.0:0.0
BP	GO:0000003	reproduction	1:0	1.0:0.0
	GO:0008152	metabolic process	39:54	37.1:49.1*
	GO:0009987	cellular process	33:55	31.4:50.0*
	GO:0010926	anatomical structure formation	1:2	1.0:1.8
	GO:0016043	cellular component organization	2:9	1.9:8.2*
	GO:0022414	reproductive process	1:0	1.0:0.0
	GO:0032501	multicellular organismal process	1:2	1.0:1.8
	GO:0032502	developmental process	1:3	1.0:2.7
	GO:0043473	pigmentation	1:11	1.0:10.0*
	GO:0044085	cellular component biogenesis	2:4	1.9:3.6
	GO:0050896	response to stimulus	3:8	2.9:7.3
	GO:0051179	localization	8:6	7.6:5.5
	GO:0065007	biological regulation	1:12	1.0:10.9*

GUPS, genes under positive selection, CC, cellular component; MF, molecular function; BP, biological process.

^*indicates remarkable difference between the gene numbers in E. siliculosus and S. japonica, when the p-value of Pearson Chi-square test is below the significant level of 0.05 (Ye et al., 2006).