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.