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.