Coexpressed gene sets of embryo and endosperm development
Using transcript datasets of WT, tissue-specific genes were clustered into co-expression modules by the k-means clustering algorithm (Howe et al., 2014). Gene ontology (GO) annotation was performed to assign genes to functional categories for each module (Ashburner et al., 2000). Twenty-two coexpression modules were generated for both embryo and endosperm (Figure 3a, b). Among these modules, 11 and 9 modules were expressed broadly at more than one stage in embryo and endosperm, respectively, indicating some common cellular processes across several stages. Overall, genes from the 11 modules of embryo and the 13 modules of endosperm were more prevalent at one out of the four developmental stages, indicating specific function of these modules at the corresponding stage.