Genome-wide signals of positive selection in strongylocentrotid sea urchins

BMC Genomics

Table 4 Significant enrichment tests for genes experiencing positive selection using the Tu et al. (2012) custom sea urchin gene ontology (GO) level 2 (L2) functional categories

		Number of genes
Category	Subcategory	Tested	PSG^a	E[PSG]^b	Fold enrichment^c	P-value^d
Adhesion	Adhesion_ECMCollagen	15	10	2.3	4.3	<0.0001
	Adhesion_ECMFibropellin	5	3	0.8	3.9	0.0632
	Adhesion_ECMNeural	13	5	2.0	2.5	0.0690
	Adhesion_ECMReceptorCadherin	14	8	2.2	3.7	0.0013
	Adhesion_ECMReceptorIgFN3	21	9	3.2	2.8	0.0056
Biomineralization	Biomineralization_Collagen	6	4	0.9	4.3	0.0168
Defensome	Defensome_TransporterABC	19	6	2.9	2.0	0.0928
Immunity	Immunity_ReceptorScavenger	21	7	3.2	2.2	0.0566
Metabolism	Metabolism_InorganicIon	107	27	16.5	1.6	0.0158
Metalloprotease	Metalloprotease	84	20	13.0	1.5	0.0599
Signaling	Signaling_Notch	10	4	1.5	2.6	0.0947

^aPositively Selected Gene
^bExpected number of PSGs
^cFold enrichment of observed PSGs to E[PSGs]
^d Empirical P-values were determined by the hypergeometric with 10,000 re-samplings from a total of 6520 genes tested and 1008 identified as PSGs

ISSN: 1471-2164