NR1I2.H12RSNP.0.M.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1I2.H12RSNP.0.M.D
Gene (human)	NR1I2 (GeneCards)
Gene synonyms (human)	PXR
Gene (mouse)	Nr1i2
Gene synonyms (mouse)	Pxr
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	19
Consensus	nbRAGTTCRhbvRGKKYdn
GC content	48.85%
Information content (bits; total / per base)	14.419 / 0.759
Data sources	Methyl-HT-SELEX
Aligned words	2483

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.869	0.854	0.803	0.791	0.702	0.703
Overall, 2 experiments	best	0.998	0.997	0.95	0.946	0.803	0.815
Methyl HT-SELEX, 1 experiments	median	0.998	0.997	0.95	0.946	0.803	0.815
Methyl HT-SELEX, 1 experiments	best	0.998	0.997	0.95	0.946	0.803	0.815
Non-Methyl HT-SELEX, 1 experiments	median	0.74	0.712	0.655	0.636	0.601	0.591
Non-Methyl HT-SELEX, 1 experiments	best	0.74	0.712	0.655	0.636	0.601	0.591

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.0.M.D.pcm
PWM	NR1I2.H12RSNP.0.M.D.pwm
PFM	NR1I2.H12RSNP.0.M.D.pfm
Alignment	NR1I2.H12RSNP.0.M.D.words.tsv
Threshold to P-value map	NR1I2.H12RSNP.0.M.D.thr
Motif in other formats
JASPAR format	NR1I2.H12RSNP.0.M.D_jaspar_format.txt
MEME format	NR1I2.H12RSNP.0.M.D_meme_format.meme
Transfac format	NR1I2.H12RSNP.0.M.D_transfac_format.txt
Homer format	NR1I2.H12RSNP.0.M.D_homer_format_0.001.txt NR1I2.H12RSNP.0.M.D_homer_format_0.0005.txt NR1I2.H12RSNP.0.M.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	467.25	482.25	891.25	642.25
02	323.25	617.25	460.25	1082.25
03	595.0	231.0	1485.0	172.0
04	2149.0	12.0	315.0	7.0
05	38.0	4.0	2441.0	0.0
06	3.0	41.0	246.0	2193.0
07	32.0	6.0	373.0	2072.0
08	8.0	2405.0	12.0	58.0
09	1290.0	16.0	1169.0	8.0
10	398.0	474.0	203.0	1408.0
11	291.0	380.0	599.0	1213.0
12	595.0	376.0	1281.0	231.0
13	1649.0	126.0	562.0	146.0
14	146.0	140.0	2038.0	159.0
15	180.0	99.0	495.0	1709.0
16	162.0	145.0	527.0	1649.0
17	149.0	1858.0	209.0	267.0
18	1047.25	194.25	1031.25	210.25
19	493.25	703.25	396.25	890.25

PFM

	A	C	G	T
01	0.188	0.194	0.359	0.259
02	0.13	0.249	0.185	0.436
03	0.24	0.093	0.598	0.069
04	0.865	0.005	0.127	0.003
05	0.015	0.002	0.983	0.0
06	0.001	0.017	0.099	0.883
07	0.013	0.002	0.15	0.834
08	0.003	0.969	0.005	0.023
09	0.52	0.006	0.471	0.003
10	0.16	0.191	0.082	0.567
11	0.117	0.153	0.241	0.489
12	0.24	0.151	0.516	0.093
13	0.664	0.051	0.226	0.059
14	0.059	0.056	0.821	0.064
15	0.072	0.04	0.199	0.688
16	0.065	0.058	0.212	0.664
17	0.06	0.748	0.084	0.108
18	0.422	0.078	0.415	0.085
19	0.199	0.283	0.16	0.359

PWM

	A	C	G	T
01	-0.283	-0.252	0.361	0.034
02	-0.65	-0.006	-0.298	0.555
03	-0.042	-0.983	0.87	-1.275
04	1.24	-3.798	-0.675	-4.242
05	-2.746	-4.65	1.367	-5.764
06	-4.834	-2.674	-0.921	1.26
07	-2.909	-4.36	-0.507	1.203
08	-4.136	1.352	-3.798	-2.34
09	0.73	-3.546	0.632	-4.136
10	-0.443	-0.269	-1.111	0.817
11	-0.754	-0.489	-0.036	0.668
12	-0.042	-0.499	0.723	-0.983
13	0.975	-1.582	-0.099	-1.437
14	-1.437	-1.479	1.187	-1.353
15	-1.23	-1.819	-0.226	1.011
16	-1.334	-1.444	-0.163	0.975
17	-1.417	1.094	-1.082	-0.84
18	0.522	-1.155	0.506	-1.077
19	-0.229	0.124	-0.447	0.36

Standard thresholds

P-value	Threshold
0.001	3.27811
0.0005	4.41371
0.0001	6.74566