NR1D1.H12RSNP.1.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1D1.H12RSNP.1.SM.D
Gene (human)	NR1D1 (GeneCards)
Gene synonyms (human)	EAR1, HREV, THRAL
Gene (mouse)	Nr1d1
Gene synonyms (mouse)	Ear1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	18
Consensus	WnYRGGTCASTRGGTCAn
GC content	50.03%
Information content (bits; total / per base)	22.393 / 1.244
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8005

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
Mouse	10 (64)	0.706	0.807	0.635	0.747	0.672	0.79	2.709	4.082	70.327	167.854

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.865	0.875	0.691	0.713	0.604	0.628
Overall, 2 experiments	best	0.947	0.951	0.746	0.767	0.638	0.664
Methyl HT-SELEX, 1 experiments	median	0.947	0.951	0.746	0.767	0.638	0.664
Methyl HT-SELEX, 1 experiments	best	0.947	0.951	0.746	0.767	0.638	0.664
Non-Methyl HT-SELEX, 1 experiments	median	0.782	0.8	0.636	0.659	0.57	0.593
Non-Methyl HT-SELEX, 1 experiments	best	0.782	0.8	0.636	0.659	0.57	0.593

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	REVERBA (NR1D) {2.1.2.3} (TFClass)
TFClass ID	TFClass: 2.1.2.3.1
HGNC	HGNC:7962
MGI	MGI:2444210
EntrezGene (human)	GeneID:9572 (SSTAR profile)
EntrezGene (mouse)	GeneID:217166 (SSTAR profile)
UniProt ID (human)	NR1D1_HUMAN
UniProt ID (mouse)	NR1D1_MOUSE
UniProt AC (human)	P20393 (TFClass)
UniProt AC (mouse)	Q3UV55 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 10 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	NR1D1.H12RSNP.1.SM.D.pcm
PWM	NR1D1.H12RSNP.1.SM.D.pwm
PFM	NR1D1.H12RSNP.1.SM.D.pfm
Alignment	NR1D1.H12RSNP.1.SM.D.words.tsv
Threshold to P-value map	NR1D1.H12RSNP.1.SM.D.thr
Motif in other formats
JASPAR format	NR1D1.H12RSNP.1.SM.D_jaspar_format.txt
MEME format	NR1D1.H12RSNP.1.SM.D_meme_format.meme
Transfac format	NR1D1.H12RSNP.1.SM.D_transfac_format.txt
Homer format	NR1D1.H12RSNP.1.SM.D_homer_format_0.001.txt NR1D1.H12RSNP.1.SM.D_homer_format_0.0005.txt NR1D1.H12RSNP.1.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3765.75	235.75	335.75	3667.75
02	1355.75	1666.75	3090.75	1891.75
03	155.0	1183.0	832.0	5835.0
04	4594.0	132.0	3243.0	36.0
05	18.0	2.0	7724.0	261.0
06	21.0	3.0	7967.0	14.0
07	19.0	83.0	387.0	7516.0
08	18.0	5856.0	14.0	2117.0
09	7954.0	2.0	29.0	20.0
10	494.0	1027.0	6227.0	257.0
11	22.0	90.0	190.0	7703.0
12	4860.0	39.0	3089.0	17.0
13	4.0	3.0	7624.0	374.0
14	46.0	18.0	7921.0	20.0
15	149.0	301.0	478.0	7077.0
16	11.0	7491.0	84.0	419.0
17	7087.5	26.5	849.5	41.5
18	2144.25	1785.25	2053.25	2022.25

PFM

	A	C	G	T
01	0.47	0.029	0.042	0.458
02	0.169	0.208	0.386	0.236
03	0.019	0.148	0.104	0.729
04	0.574	0.016	0.405	0.004
05	0.002	0.0	0.965	0.033
06	0.003	0.0	0.995	0.002
07	0.002	0.01	0.048	0.939
08	0.002	0.732	0.002	0.264
09	0.994	0.0	0.004	0.002
10	0.062	0.128	0.778	0.032
11	0.003	0.011	0.024	0.962
12	0.607	0.005	0.386	0.002
13	0.0	0.0	0.952	0.047
14	0.006	0.002	0.99	0.002
15	0.019	0.038	0.06	0.884
16	0.001	0.936	0.01	0.052
17	0.885	0.003	0.106	0.005
18	0.268	0.223	0.256	0.253

PWM

	A	C	G	T
01	0.632	-2.13	-1.78	0.605
02	-0.389	-0.183	0.434	-0.056
03	-2.545	-0.525	-0.876	1.069
04	0.83	-2.703	0.482	-3.959
05	-4.595	-6.156	1.35	-2.03
06	-4.456	-5.945	1.381	-4.815
07	-4.546	-3.157	-1.638	1.322
08	-4.595	1.073	-4.815	0.056
09	1.379	-6.156	-4.161	-4.5
10	-1.396	-0.666	1.134	-2.045
11	-4.414	-3.078	-2.344	1.347
12	0.887	-3.883	0.434	-4.645
13	-5.771	-5.945	1.337	-1.672
14	-3.726	-4.595	1.375	-4.5
15	-2.584	-1.888	-1.428	1.262
16	-5.019	1.319	-3.145	-1.559
17	1.264	-4.244	-0.855	-3.824
18	0.069	-0.114	0.026	0.01

Standard thresholds

P-value	Threshold
0.001	-3.18349
0.0005	-1.38094
0.0001	2.42026