Table 1. GO term over-representation analysis of k-means clustered genes.

Cluster	Level	GO Term	N	Gene ID
1–4	4	carbohydrate metabolic process	9	AJ625361, AJ623376, AJ626213, AJ625569, AJ625778, AJ624637, AJ624093, AJ625051, AJ625276
	3	multicellular organismal development	2	AJ626213, AJ623925
	3	catabolic process	7	AJ625525, AJ623376, AJ625569, AJ625778, AJ624637, AJ624093, AJ625051
2	2	Cellular componenet organization	8	AJ624894, AJ623937, AJ516886, AJ516796, AJ625032, AJ625091, AJ625595, AJ626097
	4	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	4	AJ624894, AJ516428, AJ623499, AJ624625
	4	carbohydrate metabolic process	3	AJ516428, AJ516541, AJ625979
	6	protein modification process	2	AJ516541, AJ625979
	3	biosynthetic process	4	AJ623499, AJ516541, AJ624625, AJ625979
	5	ion transport	2	AJ623499, AJ624625
	3	regulation of biological process	2	AJ516886, AJ624894
	4	generation of precursor metabolites and energy	2	AJ623499, AJ624625
3	5	signal transduction	5	AJ625058, AJ623860, AJ624502, AJ624437, AJ625339
	3	multicellular organismal development	9	AJ626467, AJ625058, AJ624878, AJ626179, AJ624502, AJ625655, AJ624125, AJ625893, AJ624437
	2	growth	2	AJ624878, AJ626179
	4	cell differentiation	2	AJ625058, AJ624502
	3	anatomical structure development	3	AJ625058, AJ624502, AJ625655
	2	cellular component organization	3	AJ625058, AJ624502, AJ625655
	4	anatomical structure morphogenesis	3	AJ625058, AJ624502, AJ625655
5	4	Protein metabolic process	5	AJ625244, AJ624144, AJ624363, AJ624341, AJ516741
	3	organelle organization	3	AJ516600, AJ516663, AJ516582
	3	regulation of biological process	6	AJ516600, AJ516735, AJ516895, AJ516759, AJ625244, AJ624834
	2	growth	3	AJ516895, AJ516600, AJ516759
	4	gene expression	3	AJ516600, AJ625244, AJ623532
	2	catabolic process	4	AJ625903, AJ625142, AJ624454, AJ624363
	4	anatomical structure morphogenesis	2	AJ516600, AJ516735
	3	cellular macromolecule biosynthetic process	2	AJ516600, AJ516735
	2	multicellular organismal development	3	AJ516735, AJ516895, AJ516600
6	3	response to stress	2	AJ623546, AJ624410
7	3	catabolic process	3	AJ625903, AJ625142, AJ624454
	4	carbohydrate metabolic process	2	AJ625903, AJ625142
	2	cellular process organization	2	AJ625862, AJ624454
	6	translation	9	AJ625894, AJ624593, AJ625505, AJ624922, AJ626199, AJ624426, AJ624925, AJ624454, AJ626374
	3	regulation of biological process	2	AJ624454, AJ625862
	4	generation of precursor metabolites and energy	2	AJ625903, AJ625142
8	6	transcription	3	AJ624130, AJ625043, AJ625243
	3	regulation of biological process	3	AJ624130, AJ625043, AJ625243
9	5	cellular protein process	2	AJ624501, AJ624087
10	4	symbiosis, encompassing mutualismthrough parasitism	2	AJ624509, AJ623481

Gene Ontology terms enrichment analysis was carried out comparing the GO term frequency distribution into each cluster against that in the whole microarray set (hypergeometric statistics, p<0.05). Only the lowest node per branch of the hierarchical structure of the Gene Ontology that fulfills the filter condition - cut off 2 sequences- was reported. Cluster 1 and 4 were merged into a unique group as they presented the same temporal expression patterns and only differed for the intensity. Shown are: Cluster, the number of cluster obtained from k-means analysis (see Figure 3); Level, level in the GO tee of biological processes; GO Term, over-represented feature; N, number of mussel sequences associated to each GO term; Gene ID, EMBL accession number of each sequence found.