Construction and analyzing integrated gene regulatory network:
The data of transcription factors (TF)-binding site were obtained from
the ChIP Enrichment analysis (ChEA) database (Chen et al., 2013;
Kuleshov et al., 2016).ChEA contains TF-DNA interactions data obtained
from ChIP-chip, ChIP-seq, ChIP-PET, and DamID (Chen et al., 2013;
Kuleshov et al., 2016). We perused the DEGs list in this database and
retrieved TFs that controlled the expression of DEGs and kept TFs that
contained p-value < 0.05. In the case of TFs, instead
of our criteria to find DEGs (log2 fold change >1) as a
common fold change, we set another level of filtering to identify
differentially expressed TFs (DE-TFs) by setting expression fold change
to 1.5 and selecting those as DE-TFs. Using TF-binding site data of the
DE-TFs, DE-TF expression, and DEGs, the GRNs were constructed in the
Cytoscape software. The most central TFs which regulate majority of the
downregulated genes were identified using CentisCape plugin of the
Cytoscape (Scardoni, Petterlini, & Laudanna, 2009). This plugin
considers the direct interaction of the TFs with their targets as
parameter called degree. Those TFs with highest number of target genes
will be considered as the most central TFs.