Table 1.

Validation of in silico target predictions of epigenetic regulators in shoots and roots. For each epigenetic regulator (1st column), the in silico targets from EpiNet (2nd column) were compared with experimentally determined targets (3rd column) to determine the size of overlap (4th column). Hypergeometric testing was used to determine whether the overlap was statistically significant compared to a random background, and the p-value is reported (5th column). A brief description of the experimental data and the citation is included in the last column.

	Epigenetic Regulator	No. of In Silico Targets	No. of Experimental Targets	No. of Overlapping Targets	Overlap p-Value	Sources of Experimental Data
Shoots	SYD	4936 1	133	40	0.0476	DEGs in syd-2 seedlings [63]
	UBC1	7239	82	19	0.7693	Salt stress-induced genes with lower expression in ubc1/ubc2 [65]
	UBC2	6879	82	32	0.0032	Salt stress-induced genes with lower expression in ubc1/ubc2 [65]
	JMJ30	4642	106	32	0.0004	DEGs in jmj30/jmj32 seedlings [66]
Roots	HDT1	8145	90	38	0.0066	DEGs in meristem zone of hdt1/2 root tips [62]
			114	48	0.0027	DEGs in elongation zone of hdt1/2 root tips [62]
			42	8	0.9557	DEGs in differentiated zone of hdt1/2 root tips [62]
	HDT2	8556	90	34	0.0996	DEGs in meristem zone of hdt1/2 root tips [62]
			114	42	0.1041	DEGs in elongation zone of hdt1/2 root tips [62]
			42	17	0.1220	DEGs in differentiated zone of hdt1/2 root tips [62]
	BRM	4234 1	93	26	0.0436	Downregulated genes in brm-101 seedlings [63]
	BRM	5470	4250	925	0.0003	DEGs in brm-1 leaves [67]
			5278	1127	0.0008	ChIP-Seq using pBRM::BRM-GFP in brm-1 [68]
			7761	1702	<0.0001	ChIP-Seq using pBRM::BRM-GFP in brm-1 [69]
			4831	1032	0.0014	ChIP-chip study using BRM antibody [70]
	PRMT4A	5130	5504	1082	0.0098	DEGs in prmt4a/prmt4b seedlings [71]

¹: in silico targets were filtered based on microarray probes.