Cellular processes in the developing embryo
Cellular processes characterizing each developmental stage were identified by GO terms that were overrepresented at particular coexpression modules (Figures 3a, S5a). The early stage of Em-S1, best represented by modules DP1-DP5, is typified by the overrepresentation for GO term Ran GTPase binding, mitotic cell cycle, nuclear division, nuclear DNA replication, cell wall organization or biogenesis, cell differentiation, mitochondrial protein complex and tricarboxylic acid cycle. Em-S2 featured modules DP6 and DP7 that were enriched in GO term characteristic of embryo enlargement, including the cell division, cell wall organization or biogenesis and lipid droplet. The module DP8 presented an up-regulation of genes involved in nutrient reservoir activity and response to external biotic stimulus, suggesting the maturation of embryo characterized by Em-S3. Stage Em-S4, represented by modules DP9-DP11, was characterized by the overrepresentation of genes involved in response to biotic stimulus (heat and light), structural constituent of ribosome, mitochondrial matrix, vacuole organization and photomorphogenesis. In addition, some genes expressed broadly in embryo across the sampled time points. All such genes were included in modules DP12-DP22, and were mostly related to protein complex, Golgi apparatus, protein kinase activity, cellular response to stimulus, RNA modification, ribosome biogenesis and endonuclease activity.