Table 1. Singular enrichment analysis (SEA) using AGriGO for genes more than two-fold differently expressed in psy2l versus WT.

GO terms of special interest for the phenotype observed are presented. Genes were sorted as Up or Down- regulated. Non-significant is marked as ns. Input number for two-fold up-regulated genes were 1227 and 1196, and two-fold down-regulated were 1290 and 1793 genes for rosette leaves and seedlings, respectively. Number of genes in background reference (BG/Ref) is given for each GO term. Total annotated number in background reference was 31819 genes.

Description/GO term	Up or down-regulated	Rosette number of genes	Seedling number of genes	BG/ref	p-value Rosette	p-value Seedling	Shared genes
MOLECULAR FUNCTION
Kinase activity GO:0016301	Up	37	57	417	8.00E-06	2.50E-15	12
	Down	93	83	417	5.20E-36	2.70E-20	21
Protein tyrosine kinase activity GO:0004713	Up	9	12	33	1.90E-05	4.60E-08	3
	Down	14	19	33	1.80E-09	8.40E-12	3
Protein Ser/Thr phosphatase activity GO:0004722	Up	15	12	58	6.20E-08	7.40E-06	4
	Down	ns	10	58	ns	3.10E-03
BIOLOGICAL PROCESS
Anatomical structure and development GO: 0048856	Up	74	70	330	2.60E-30	4.10E-28	22
	Down	35	67	330	1.10E-06	5.20E-17	9
Response to hormone stimulus GO:0009725	Up	63	64	755	4.90E-08	8.80E-09	18
	Down	68	85	755	5.90E-09	1.30E-08	18
Response to abscisic acid stimulus GO:0009737	Up	37	40	276	6.30E-10	7.40E-12	15
	Down	ns	ns	276	ns	ns
Response to ethylene GO:0009723	Up	9	12	30	1.00E-05	2.00E-08	1
	Down	17	7	30	9.00E-13	3.10E-03	3
Response to gibberellin stimulus GO:0009739	Up	11	7	19	5.00E-09	2.90E-05	3
	Down	16	10	19	5.20E-14	1.40E-06	6
Response to cytokinin stimulus GO:0009735	Up	ns	ns	72	ns	ns
	Down	11	15	72	3.70E-04	5.30E-05	5
Flavonoid biosynthetic process GO:0009813	Up	16	9	61	1.90E-08	9.30E-04	7
	Down	ns	ns	61	ns	ns
Transport GO:0006810	Up	89	69	540	1.40E-27	6.40E-17	24
	Down	93	107	540	1.80E-28	1.10E-25	23
CELLULAR COMPONENT
Nucleus GO:0005634	Up	107	99	212	7.2E-72	4.8E-65	31
	Down	74	98	212	1.4E-39	1.2E-48	18