Table 2.

This table depicts the top five ranked edges from the PEN created using iRF-LOOP on A. thaliana expression data. None of the edges were true positive edges in the gold standard network, but have some existing biological relationship. This table shows that PENs produced with iRF-LOOP capture relationships beyond simple gene regulation.

Rank	Impor-tance Score	Start Gene – End Gene ID	Start Gene – End Gene Function	Relationship
1	0.970	AT5G05430 — AT5G05420	RNA-binding protein — FKBP-like peptidyl-prolyl cis–trans isomerase family protein	Endosperm specific genes [23]
2	0.962	ArthCt101 — ArthCt092	Transfer RNA — Transfer RNA	Noncoding transfer RNAs, both in Aminoacyl-tRNA biosynthesis pathway [24]
3	0.959	AT3G28550 — AT1G23720	Proline rich extensin like family protein — Proline rich extensin like family protein	EXT genes in cell wall [25]
4	0.949	ArthCt092 — ArthCt101	Transfer RNA — Transfer RNA	Noncoding transfer RNAs, both in Aminoacyl-tRNA biosynthesis pathway [24]
5	0.941	AT5G44120 — AT4G28520	RmlC-like cupins superfamily protein — Cruciferin 3	Seed storage proteins that are down and up regulated together, both contribute to hexamer formation [26], [27]