Table 5. Enriched GO Terms in Aleurone Direct Target Genes.

GO Term	Ontology	Description	DE AL Genesa	AL Transcriptomeb	P Valuec	FDRd
NKD2
GO:0045735	F	Nutrient reservoir activity	22	56	2.80E-18	1.70E-15
GO:0032993	C	Protein-DNA complex	14	106	1.30E-05	0.0059
GO:0000786	C	Nucleosome	13	101	3.40E-05	0.0077
GO:0034728	P	Nucleosome organization	14	107	1.40E-05	0.0085
GO:0006334	P	Nucleosome assembly	14	107	1.40E-05	0.0085
GO:0031497	P	Chromatin assembly	14	109	1.80E-05	0.0085
GO:0065004	P	Protein-DNA complex assembly	14	110	2.00E-05	0.0085
GO:0006333	P	Chromatin assembly or disassembly	14	111	2.20E-05	0.0085
GO:0006323	P	DNA packaging	14	115	3.20E-05	0.011
GO:0071103	P	DNA conformation change	16	152	5.70E-05	0.016
GO:0009536	C	Plastid	104	2144	0.00026	0.029
GO:0000785	C	Chromatin	13	122	0.00024	0.029
GO:0046982	F	Protein heterodimerization activity	15	148	0.00014	0.044
GO:0044427	C	Chromosomal part	15	173	0.00077	0.07
GO:0009507	C	Chloroplast	96	2036	0.00095	0.072
GO:0005773	C	Vacuole	45	818	0.0011	0.072
GO:0005694	C	Chromosome	17	230	0.0021	0.12
GO:0019252	P	Starch biosynthetic process	5	21	0.00053	0.13
GO:0050660	F	FAD binding	13	135	0.00063	0.13
GO:0044435	C	Plastid part	57	1142	0.0025	0.13
GO:0003774	F	Motor activity	10	95	0.0013	0.16
GO:0003777	F	Microtubule motor activity	9	79	0.0013	0.16
GO:0005875	C	Microtubule associated complex	9	92	0.0037	0.17
GO:0009579	C	Thylakoid	29	513	0.0049	0.17
GO:0044434	C	Chloroplast part	55	1125	0.0044	0.17
GO:0015630	C	Microtubule cytoskeleton	14	189	0.0048	0.17
GO:0044422	C	Crganelle part	135	3190	0.0058	0.18
GO:0044446	C	Intracellular organelle part	135	3187	0.0056	0.18
GO:0004553	F	Hydrolase activity, hydrolyzing O-glycosyl compounds	24	371	0.0019	0.19
NKD
GO:0045735	F	Nutrient reservoir activity	21	56	6.50E-19	3.50E-16

The number of each GO term occurrence in differentially expressed AL genes with a motif in proximal promoter region and in RNA-seq AL detected (transcriptome) genes was determined. GO enrichment in DE genes with a motif was assessed relative to the transcriptome. GO enrichment was not detected for NKD1 AL direct target genes. See Supplemental Data Sets 3 and 4 for further details.

^aNumber of putative direct target genes expressed in the aleurone associated with each GO term.

^bTotal number of genes in each GO category expressed in the aleurone transcriptome.

^cFisher’s exact test for GO term enrichment.

^dFalse discovery rate.