Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes

BMC Bioinformatics

Table 1 Top 25 transcription factors ranked by DL\(\times\)JTK metric

Rank	S. cerevisiae		M. Musculus		A. thaliana
Rank	MA	RNA	MA	RNA	LDHC	LL_LDHC
1	SWI5*	TOS4*	ARNTL*	DBP*	COL1	STH
2	YOX1*	HST4	DBP*	NPAS2*	HB-12	AT1G26790
3	HST3	HST3	NPAS2*	CDX4	TGA3	CCA1*
4	ASF1	SWI5*	NR1D1*	ARNTL*	RVE1	BBX18
5	ACE2*	YOX1*	NR1D2*	EGR1	MYBL2	COL1
6	RTT107	RTT107	BHLHE41*	GM14401	LHY*	CDF1
7	STB1*	WTM2	CLOCK*	GM14305	CO	COL2
8	HCM1*	ASH1*	NFIL3*	POU4F1	PIL6	CDF3
9	RME1	FKH1*	RFXANK	EN2	AT2G28200	AT2G28200
10	FKH1*	ASF1	RORC*	DMRTA2	COL2	RVE1
11	PLM2*	ACE2*	TEF*	LHX1	CCA1*	LHY*
12	SWI4*	POG1	CREM	GM20422	PRR7*	COL5
13	NDD1*	SWI4*	EGR1	GM14444	HYH	PIF4
14	ASH1*	RME1	PPARD	OVOL2	BBX18	PIL6
15	YHP1*	PLM2*	ZBTB21	GM4969	RVE8*	BBX16
16	TOS4*	RLF2	NFIC	HOXC4	PRE1	LUX*
17	EDS1	NDD1*	AHCTF1	FOXO6	BZS1	PRR7*
18	RIF1	HCM1*	ATF5	MESP1	EPR1	CDF2
19	SIP4	GAT1	LITAF	AI854703	CDF3	LZF1
20	FHL1*	TEC1	KLF10	NR1D1*	RVE2	HB-12
21	NUT1	STB1*	KLF13	BNC2	AT1G26790	RVE8*
22	ASG1	YHP1*	ESR1	NPAS3	BBX16	ATCTH
23	TBF1	RPI1	STAT5B	2210418O10RIK	COL9	MYBL2
24	SNF5	MTH1	SREBF1	HOXC6	LZF1	ARF11
25	WTM2	RIF1	MAFB	TBX1	ARF10	RL6
Recall	76.5%	70.6%	66.7%	28.6%	36.4%	45.5%

LL_LDHC: Constant light and temperature; LDHC: 24 hour cycling light and temperature; MA: Microarray; RNA: RNAseq
*Core transcription factors in Additional file 2—Core Genes

ISSN: 1471-2105