TABLE 1.

Summary statistics of the upstream transcription factor (TF) enrichment analysis for the Arabidopsis gene set bound by LHY (Adams et al., 2018).

TF ID (AGI ID)	xa	nb	Observed (%)	Xc	Nd	Expected (%)	p-Value	Corrected p-valuee	Gene symbols	Gene names
AT5G02840	287	722	39.8	4,110	27,206	15.1	5.84 × 10–60	2.04 × 10–57	LCL1	LHY/CCA1-LIKE 1
AT3G09600	426	722	59.0	8,276	27,206	30.4	2.59 × 10–58	4.52 × 10–56	RVE8, LCL5	LHY-CCA1-LIKE5, REVEILLE 8
AT3G56850	275	722	38.1	3,936	27,206	14.5	6.43 × 10–57	7.48 × 10–55	AREB3, DPBF3	ABA-RESPONSIVE ELEMENT BINDING PROTEIN 3
AT2G46270	318	722	44.0	5,255	27,206	19.3	2.09 × 10–53	1.82 × 10–51	GBF3	G-BOX BINDING FACTOR 3
AT1G01060	517	722	71.6	11,896	27,206	43.7	3.01 × 10–53	2.10 × 10–51	LHY	LATE ELONGATED HYPOCOTYL
AT2G36270	274	722	38.0	4,188	27,206	15.4	8.13 × 10–51	4.73 × 10–49	ABI5, GIA1	GROWTH-INSENSITIVITY TO ABA 1, ABA INSENSITIVE 5
AT3G62420	327	722	45.3	5,764	27,206	21.2	7.54 × 10–49	3.76 × 10–47	BZIP53	BASIC REGION/LEUCINE ZIPPER MOTIF 53
AT1G18330	619	722	85.7	16,878	27,206	62.0	3.63 × 10–46	1.58 × 10–44	EPR1, RVE7	EARLY-PHYTOCHROME-RESPONSIVE 1, REVEILLE 7
AT5G17300	585	722	81.0	15,403	27,206	56.6	6.78 × 10–45	2.63 × 10–43	RVE1	REVEILLE 1
AT1G32150	357	722	49.4	6,979	27,206	25.7	6.05 × 10–44	2.11 × 10–42	bZIP68	BASIC REGION/LEUCINE ZIPPER TRANSCRIPTION FACTOR 68
AT4G34590	381	722	52.8	7,781	27,206	28.6	1.94 × 10–43	6.15 × 10–42	GBF6, BZIP11, ATB2	ARABIDOPSIS THALIANA BASIC LEUCINE-ZIPPER 11, G-BOX BINDING FACTOR 6
AT5G52660	224	722	31.0	3,280	27,206	12.1	6.20 × 10–43	1.80 × 10–41
AT5G15830	336	722	46.5	6,440	27,206	23.7	2.94 × 10–42	7.88 × 10–41	bZIP3	BASIC LEUCINE-ZIPPER 3
AT2G18160	178	722	24.7	2,268	27,206	8.3	4.60 × 10–41	1.15 × 10–39	GBF5, bZIP2, ATBZIP2, FTM3	BASIC LEUCINE-ZIPPER 2, FLORAL TRANSITION AT THE MERISTEM3, G-BOX BINDING FACTOR 5
AT4G01280	339	722	47.0	6,654	27,206	24.5	1.88 × 10–40	4.38 × 10–39
AT3G10113	579	722	80.2	15,664	27,206	57.6	6.91 × 10–39	1.51 × 10–37
AT1G45249	165	722	22.9	2,112	27,206	7.8	1.45 × 10–37	2.98 × 10–36	ABF2, AREB1	ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING PROTEIN 1, ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING FACTOR 2
AT3G10800	132	722	18.3	1,469	27,206	5.4	7.86 × 10–36	1.52 × 10–34	BZIP28
AT4G36780	269	722	37.3	4,944	27,206	18.2	1.02 × 10–34	1.88 × 10–33	BEH2	BES1/BZR1 HOMOLOG 2
AT2G35530	137	722	19.0	1,630	27,206	6.0	3.89 × 10–34	6.79 × 10–33	bZIP16	BASIC REGION/LEUCINE ZIPPER TRANSCRIPTION FACTOR 16

^aThe number of genes bound by the specific TF in the test set. ^bThe number of genes in the test set. ^cThe number of genes bound by the specific TF in the reference set. ^dThe number of genes in the reference set. ^eThe p-value after Bonferroni or Benjamini-Hochberg correction.