Table 3. Gene ontology analysis on MMC and AIC.

A) Arabidopsis thaliana MMC
GO.ID	Term	Annotated	Significant	Expected	p value
GO:0016538	cyclin-dependent protein kinase regulator activity	29	6	1.14	0.00081
GO:0005199	structural constituent of cell wall	30	6	1.18	0.00098
GO:0016844	strictosidine synthase activity	14	4	0.55	0.00176
GO:0004129	cytochrome-c oxidase activity	15	4	0.59	0.00232
GO:0010178	IAA-amino acid conjugate hydrolase activity	3	2	0.12	0.00455
GO:0003743	translation initiation factor activity	82	9	3.24	0.00496
GO:0005034	osmosensor activity	4	2	0.16	0.00885

Significant upregulation of molecular functions based on 852 genes expressed in the Arabidopsis MMC but not in the Boechera AIC (A). Significant upregulation of molecular functions based on 901 genes expressed in the apomictic initial cell but not in the MMC (B). A p value<0.01 was considered significant.