NR1I2.H12RSNP.1.S.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1I2.H12RSNP.1.S.D
Gene (human)	NR1I2 (GeneCards)
Gene synonyms (human)	PXR
Gene (mouse)	Nr1i2
Gene synonyms (mouse)	Pxr
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	12
Consensus	nbRAGTTCAbdn
GC content	47.92%
Information content (bits; total / per base)	11.351 / 0.946
Data sources	HT-SELEX
Aligned words	599

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.854	0.813	0.802	0.762	0.721	0.697
Overall, 2 experiments	best	0.952	0.924	0.905	0.872	0.799	0.781
Methyl HT-SELEX, 1 experiments	median	0.952	0.924	0.905	0.872	0.799	0.781
Methyl HT-SELEX, 1 experiments	best	0.952	0.924	0.905	0.872	0.799	0.781
Non-Methyl HT-SELEX, 1 experiments	median	0.757	0.702	0.699	0.652	0.642	0.613
Non-Methyl HT-SELEX, 1 experiments	best	0.757	0.702	0.699	0.652	0.642	0.613

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	VDR (NR1I) {2.1.2.4} (TFClass)
TFClass ID	TFClass: 2.1.2.4.2
HGNC	HGNC:7968
MGI	MGI:1337040
EntrezGene (human)	GeneID:8856 (SSTAR profile)
EntrezGene (mouse)	GeneID:18171 (SSTAR profile)
UniProt ID (human)	NR1I2_HUMAN
UniProt ID (mouse)	NR1I2_MOUSE
UniProt AC (human)	O75469 (TFClass)
UniProt AC (mouse)	O54915 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	NR1I2.H12RSNP.1.S.D.pcm
PWM	NR1I2.H12RSNP.1.S.D.pwm
PFM	NR1I2.H12RSNP.1.S.D.pfm
Alignment	NR1I2.H12RSNP.1.S.D.words.tsv
Threshold to P-value map	NR1I2.H12RSNP.1.S.D.thr
Motif in other formats
JASPAR format	NR1I2.H12RSNP.1.S.D_jaspar_format.txt
MEME format	NR1I2.H12RSNP.1.S.D_meme_format.meme
Transfac format	NR1I2.H12RSNP.1.S.D_transfac_format.txt
Homer format	NR1I2.H12RSNP.1.S.D_homer_format_0.001.txt NR1I2.H12RSNP.1.S.D_homer_format_0.0005.txt NR1I2.H12RSNP.1.S.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	116.75	109.75	230.75	141.75
02	78.75	152.75	127.75	239.75
03	202.0	26.0	359.0	12.0
04	557.0	5.0	26.0	11.0
05	0.0	0.0	599.0	0.0
06	0.0	0.0	70.0	529.0
07	0.0	0.0	7.0	592.0
08	0.0	597.0	1.0	1.0
09	407.0	0.0	192.0	0.0
10	57.0	185.0	77.0	280.0
11	84.25	75.25	256.25	183.25
12	108.5	168.5	179.5	142.5

PFM

	A	C	G	T
01	0.195	0.183	0.385	0.237
02	0.131	0.255	0.213	0.4
03	0.337	0.043	0.599	0.02
04	0.93	0.008	0.043	0.018
05	0.0	0.0	1.0	0.0
06	0.0	0.0	0.117	0.883
07	0.0	0.0	0.012	0.988
08	0.0	0.997	0.002	0.002
09	0.679	0.0	0.321	0.0
10	0.095	0.309	0.129	0.467
11	0.141	0.126	0.428	0.306
12	0.181	0.281	0.3	0.238

PWM

	A	C	G	T
01	-0.246	-0.307	0.429	-0.054
02	-0.633	0.02	-0.157	0.467
03	0.297	-1.702	0.868	-2.41
04	1.306	-3.133	-1.702	-2.486
05	-4.55	-4.55	1.378	-4.55
06	-4.55	-4.55	-0.749	1.254
07	-4.55	-4.55	-2.868	1.367
08	-4.55	1.375	-4.065	-4.065
09	0.993	-4.55	0.246	-4.55
10	-0.949	0.209	-0.655	0.621
11	-0.567	-0.678	0.533	0.2
12	-0.318	0.117	0.179	-0.049

Standard thresholds

P-value	Threshold
0.001	4.17666
0.0005	5.396265
0.0001	7.72478