Among the 44 total putative target genes, 9 transcription factors (27.5%), including OsSMF1, were observed, which were assigned to "regulation of nitrogen compound metabolic process (GO 0051171, Table 2).
Further, 10 transcription factors, including OsSMF1, were assigned to "regulation of nitrogen compound metabolic process (GO 0051171)." Among these transcription factors, two, including OsGZF1 and rice prolamin box-binding factor (RPBF), were co-expressed with OsSMF1 (Chen et al. 2014; Yamamoto et al. 2006).
The majority of the ESTs (almost 80%) were dedicated to cellular and physiological processes in the biological process category, with an additional 11% assigned to regulation of the biological processes (Figure 5A).
Additionally, four proteins which are exclusively assigned to regulation of cell death were included.
For each interaction, we randomly assigned a regulation order of 0, 1, 2 or 3. We used two different conditional probabilities for the interactions between the genes, namely, the noisy regulation according to a binomial distribution and the noisy XOR-style co-regulation.
For single-peptide identified proteins, up- and down-regulation were assigned when the regulation factors were above 1.5 folds (p < 0.05) [ 16].
GO annotation showed that many transcripts were assigned to regulation-related process such as response to stress and wounding and defence responses in the biological process category.
To assign gene regulation in the CAM to specific cell types (EC vs. Non-EC: stromal cells), we relied on a recent bioinformatic approach.
Additionally, we selected transcripts assigned to negative regulation of apoptosis.
Additional large group of genes were assigned to protein regulation and metabolism.
