NR1H4.H12INVITRO.0.P.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1H4.H12INVITRO.0.P.D
Gene (human)	NR1H4 (GeneCards)
Gene synonyms (human)	BAR, FXR, HRR1, RIP14
Gene (mouse)	Nr1h4
Gene synonyms (mouse)	Bar, Fxr, Rip14
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	20
Consensus	RGKKSAvYGvCCbbvvKKnY
GC content	62.34%
Information content (bits; total / per base)	12.93 / 0.646
Data sources	ChIP-Seq
Aligned words	918

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	2 (14)	0.928	0.932	0.875	0.888	0.879	0.888	3.724	3.827	303.882	357.638
Mouse	4 (20)	0.887	0.913	0.854	0.872	0.859	0.887	3.766	4.0	509.934	634.886

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	Nuclear receptors with C4 zinc fingers {2.1} (TFClass)
TF family	Thyroid hormone receptor-related {2.1.2} (TFClass)
TF subfamily	LXR (NR1H) {2.1.2.7} (TFClass)
TFClass ID	TFClass: 2.1.2.7.3
HGNC	HGNC:7967
MGI	MGI:1352464
EntrezGene (human)	GeneID:9971 (SSTAR profile)
EntrezGene (mouse)	GeneID:20186 (SSTAR profile)
UniProt ID (human)	NR1H4_HUMAN
UniProt ID (mouse)	NR1H4_MOUSE
UniProt AC (human)	Q96RI1 (TFClass)
UniProt AC (mouse)	Q60641 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 4 mouse
HT-SELEX	0
Methyl-HT-SELEX	0

PCM	NR1H4.H12INVITRO.0.P.D.pcm
PWM	NR1H4.H12INVITRO.0.P.D.pwm
PFM	NR1H4.H12INVITRO.0.P.D.pfm
Alignment	NR1H4.H12INVITRO.0.P.D.words.tsv
Threshold to P-value map	NR1H4.H12INVITRO.0.P.D.thr
Motif in other formats
JASPAR format	NR1H4.H12INVITRO.0.P.D_jaspar_format.txt
MEME format	NR1H4.H12INVITRO.0.P.D_meme_format.meme
Transfac format	NR1H4.H12INVITRO.0.P.D_transfac_format.txt
Homer format	NR1H4.H12INVITRO.0.P.D_homer_format_0.001.txt NR1H4.H12INVITRO.0.P.D_homer_format_0.0005.txt NR1H4.H12INVITRO.0.P.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	478.0	19.0	394.0	27.0
02	78.0	12.0	788.0	40.0
03	77.0	19.0	690.0	132.0
04	30.0	72.0	262.0	554.0
05	16.0	674.0	136.0	92.0
06	735.0	54.0	102.0	27.0
07	357.0	224.0	211.0	126.0
08	38.0	128.0	60.0	692.0
09	65.0	34.0	816.0	3.0
10	497.0	105.0	222.0	94.0
11	70.0	790.0	29.0	29.0
12	84.0	758.0	4.0	72.0
13	49.0	347.0	224.0	298.0
14	171.0	372.0	185.0	190.0
15	179.0	208.0	368.0	163.0
16	298.0	227.0	315.0	78.0
17	92.0	30.0	676.0	120.0
18	73.0	70.0	649.0	126.0
19	135.0	209.0	258.0	316.0
20	47.0	613.0	92.0	166.0

PFM

	A	C	G	T
01	0.521	0.021	0.429	0.029
02	0.085	0.013	0.858	0.044
03	0.084	0.021	0.752	0.144
04	0.033	0.078	0.285	0.603
05	0.017	0.734	0.148	0.1
06	0.801	0.059	0.111	0.029
07	0.389	0.244	0.23	0.137
08	0.041	0.139	0.065	0.754
09	0.071	0.037	0.889	0.003
10	0.541	0.114	0.242	0.102
11	0.076	0.861	0.032	0.032
12	0.092	0.826	0.004	0.078
13	0.053	0.378	0.244	0.325
14	0.186	0.405	0.202	0.207
15	0.195	0.227	0.401	0.178
16	0.325	0.247	0.343	0.085
17	0.1	0.033	0.736	0.131
18	0.08	0.076	0.707	0.137
19	0.147	0.228	0.281	0.344
20	0.051	0.668	0.1	0.181

PWM

	A	C	G	T
01	0.73	-2.413	0.537	-2.086
02	-1.065	-2.826	1.228	-1.713
03	-1.078	-2.413	1.096	-0.548
04	-1.987	-1.143	0.132	0.877
05	-2.569	1.072	-0.518	-0.903
06	1.159	-1.423	-0.802	-2.086
07	0.439	-0.024	-0.083	-0.594
08	-1.762	-0.578	-1.321	1.099
09	-1.243	-1.868	1.263	-3.895
10	0.769	-0.773	-0.033	-0.882
11	-1.171	1.231	-2.019	-2.019
12	-0.992	1.19	-3.702	-1.143
13	-1.517	0.411	-0.024	0.259
14	-0.292	0.48	-0.214	-0.187
15	-0.246	-0.098	0.469	-0.339
16	0.259	-0.011	0.315	-1.065
17	-0.903	-1.987	1.075	-0.642
18	-1.13	-1.171	1.035	-0.594
19	-0.525	-0.093	0.116	0.318
20	-1.558	0.978	-0.903	-0.321

Standard thresholds

P-value	Threshold
0.001	4.03271
0.0005	4.96351
0.0001	6.92986