Table 3.

This table depicts a sample of three highly prevalent sets determined using RIT on the resulting paths from iRF-LOOP on A. thaliana expression data. All three of these sets have been found to have some known biological relationship. None of these sets were found in the gold standard network, while some were found in the iRF-LOOP PEN as edges with low importance scores. This shows that RIT combined with iRF-LOOP can be used to discover or validate gene to gene relationships in sets.

Prev-alence	Gene ID	Function	Target	Target Function	Relation-ship
0.966	AT3G44630 – AT3G44400	Both disease resistance protein (TIR-NBS-LRR class) family	AT3G44480	Encodes a TIR-NB-LRR R-protein RPP1 that confers resistance to Peronospora parasitica	All three encode disease resistant proteins, regulation is linked in some experiments [28]
0.964	AT3G28550 – AT3G54590	Proline-rich extensin-like family protein – Hydroxy-proline-rich glycoprotein	AT3G54580	Proline-rich extensin-like family protein	EXT genes in cell wall [25]
0.957	AT3G44480 – AT3G44630	Both disease resistance protein (TIR-NBS-LRR class) family	AT3G44400	Disease resistance protein (TIR-NBS-LRR class) family	All three encode disease resistant proteins