Table 6. Enriched GO Terms in Starchy Endosperm Direct Target Genes.

GO Term	Ontology	Description	DE SE Genesa	SE Transcriptomeb	P Valuec	FDRd
NKD1
GO:0030312	C	External encapsulating structure	12	596	0.0011	0.12
GO:0005618	C	Cell wall	12	579	0.00084	0.12
GO:0048046	C	Apoplast	8	324	0.002	0.14
NKD2
GO:0009536	C	Plastid	118	2128	2.40E-06	0.0012
GO:0045735	F	Nutrient reservoir activity	12	67	3.10E-06	0.0021
GO:0009507	C	Chloroplast	107	2023	3.80E-05	0.0097
GO:0044435	C	Plastid part	63	1128	0.00027	0.046
GO:0005618	C	Cell wall	36	579	0.00075	0.082
GO:0044434	C	Chloroplast part	60	1111	0.00081	0.082
GO:0030312	C	External encapsulating structure	36	596	0.0012	0.1
NKD
GO:0005618	C	Cell wall	27	579	0.00053	0.15
GO:0030312	C	External encapsulating structure	27	596	0.00081	0.15

The number of each GO term occurrence in differentially expressed SE genes with a motif in proximal promoter region and in RNA-seq SE detected (transcriptome) genes was determined. GO enrichment in DE genes with a motif was assessed relative to the transcriptome. See Supplemental Data Sets 3 and 4 for further details.

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

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

^cFisher’s exact test for GO term enrichment.

^dFalse discovery rate.