. 2016 Mar 3;8(3):851–870. doi: 10.1093/gbe/evw042

Table 1.

GO Enrichment Summary in Complete Data Sets and Consecutive Stages Developmental Progressions

	Stage^a	GO ID	Node Size	Sample Match	P Adj	Term	Ontology
General GO enrichment	PC	GO:0043295	36	29	3.82.E−02	Glutathione binding	MF
	G	GO:0019003	97	67	2.81.E−02	GDP binding	MF
	S	GO:0008134	1105	641	3.21.E−05	Transcription factor binding	MF
	P	GO:0004616	25	22	7.30.E−03	Phosphogluconate dehydrogenase (decarboxylating) activity	MF
	A	GO:0004407	27	23	4.82.E−02	Histone deacetylase activity	MF
	A	GO:0004683	406	223	3.64.E−02	Calmodulin-dependent protein kinase activity	MF
	PC_A	GO:0005083	586	317	7.20.E−03	Small gtpase regulator activity	MF
	PC_S	GO:0008013	155	102	1.58.E−02	Beta-catenin binding	MF
	PC_G_P_A	GO:0070491	108	301	2.51.E−03	Repressing transcription factor binding	MF
	PC_S_P_A	GO:0007030	404	263	3.33.E−12	Golgi organization	BP
	All	GO:0030258	677	416	9.48.E−13	Lipid modification	BP
		GO:0006907	2,415	1,469	3.90.E−51	Pinocytosis
		GO:0006396	28,24	1,669	1.91.E−40	RNA processing

^aEnriched in stages shown in column. Node size = Total number of Go terms in node. Sample match = number of transcripts with GO terms associated to specific nodes.

	Comparison	Up in^a	GO ID	Node Size	Sample match	P adj	Term	Ontology
DEGs GO enrichment	PC vs. G	PC	GO:0043407	185	41	9.42.E−06	Negative regulation of MAP kinase activity	BP
			GO:0007264	1,493	166	4.09.E−02	Small GTPase mediated signal transduction
			GO:0050854	70	20	1.87.E−03	Regulation of antigen receptor-mediated signaling pathway
			GO:0033209	123	27	6.51.E−03	Tumor necrosis factor-mediated signaling pathway
		G	GO:0000184	354	92	2.98.E−11	Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
			GO:0000462	209	58	1.13.E−07	Maturation of ssu-rRNA from tricistronic rRNA transcript
			GO:0001510	376	96	2.67.E−11	RNA methylation
			GO:0008168	795	174	4.46.E−03	Methyltransferase activity	MF
	G vs. S	S	GO:0030855	1,125	181	1.35.E−03	Epithelial cell differentiation	BP
			GO:0021575	141	39	1.36.E−04	Hindbrain morphogenesis
			GO:0048732	1,502	223	2.65.E−02	Gland development
			GO:0048644	537	97	4.35.E−03	Muscle organ morphogenesis
	S vs. P	S	GO:0060070	757	130	5.42.E−06	Canonical wnt receptor signaling pathway	BP
			GO:0002119	798	135	7.17.E−06	Nematode larval development
			GO:0007626	1,158	187	6.86.E−04	Locomotory behavior
		P	GO:0006334	178	28	7.59.E−03	Nucleosome assembly
	P vs. A	P	GO:0001510	376	96	2.67.E−11	RNA methylation	BP
		P	GO:0042775	95	21	7.48.E−04	Mitochondrial ATP synthesis coupled electron transport
		A	GO:0045216	573	77	4.45.E−04	Cell-cell junction organization
			GO:0007049	6,219	1,019	2.27.E−11	Cell cycle
			GO:0002433	282	73	3.49.E−05	Immune resp. cell surface receptor signaling pathway involved in phagocytosis
			GO:0007292	2,123	356	9.30.E−03	Female gamete generation
			GO:0019954	831	165	3.01.E−04	Asexual reproduction
			GO:0008543	490	99	3.91.E−02	Fibroblast growth factor receptor signaling pathway
			GO:0032319	425	57	2.24.E−02	Regulation of rho GTPase activity

Enriched in stages shown in column. Node size= Total number of GO terms in node. Sample match = number of transcripts with GO terms associated to specific nodes. GO categories shown in this table were selected based on: 1) significant P values (0.05 cutoff value) and 2) evidence in the literature of their involvement in the regulation of developmental processes. A complete list of enriched GO categories can be found in supplementary file S4, Supplementary Material online.