Gene coexpression and functional enrichment analysis
The co-expression analysis for genes in embryo and endosperm was
conducted using MeV (Howe et al., 2014). Notably, we used the Z-score
value to calculate the relative expression levels before running the MeV
for a tissue. These Z-score values were used as input for MeV and each
individual dataset was clustered using the k-means method and Pearson
correlation coefficients among the genes. Eventually, through Gene
Ontology (GO) annotation (Ashburner
et al., 2000), genes were annotated into the functional categories, and
functional enrichment analysis was performed using the phyper function
in R software with default setting (R Core Team, 2013). P-value was used
as a filter mode, and significant GO categories (P-value
<0.01) were identified. In addition, embryo or endosperm
specific genes were identified by Z-score value. A gene was declared as
embryo or endosperm specific if it had a Z-score above 2 in at least one
of the embryo or endosperm samples as compared to all the same kind
samples.