NR1D1.H12INVITRO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1D1.H12INVITRO.0.P.B
Gene (human)	NR1D1 (GeneCards)
Gene synonyms (human)	EAR1, HREV, THRAL
Gene (mouse)	Nr1d1
Gene synonyms (mouse)	Ear1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	15
Consensus	MWbbRGGYCAvhddv
GC content	52.29%
Information content (bits; total / per base)	11.203 / 0.747
Data sources	ChIP-Seq
Aligned words	1000

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)	0.739	0.894	0.691	0.829	0.724	0.874	2.783	3.674	76.062	219.377

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.859	0.865	0.681	0.705	0.591	0.62
Overall, 2 experiments	best	0.943	0.943	0.737	0.76	0.622	0.654
Methyl HT-SELEX, 1 experiments	median	0.943	0.943	0.737	0.76	0.622	0.654
Methyl HT-SELEX, 1 experiments	best	0.943	0.943	0.737	0.76	0.622	0.654
Non-Methyl HT-SELEX, 1 experiments	median	0.775	0.787	0.625	0.65	0.559	0.585
Non-Methyl HT-SELEX, 1 experiments	best	0.775	0.787	0.625	0.65	0.559	0.585

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.H12INVITRO.0.P.B.pcm
PWM	NR1D1.H12INVITRO.0.P.B.pwm
PFM	NR1D1.H12INVITRO.0.P.B.pfm
Alignment	NR1D1.H12INVITRO.0.P.B.words.tsv
Threshold to P-value map	NR1D1.H12INVITRO.0.P.B.thr
Motif in other formats
JASPAR format	NR1D1.H12INVITRO.0.P.B_jaspar_format.txt
MEME format	NR1D1.H12INVITRO.0.P.B_meme_format.meme
Transfac format	NR1D1.H12INVITRO.0.P.B_transfac_format.txt
Homer format	NR1D1.H12INVITRO.0.P.B_homer_format_0.001.txt NR1D1.H12INVITRO.0.P.B_homer_format_0.0005.txt NR1D1.H12INVITRO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	611.0	250.0	49.0	90.0
02	681.0	20.0	31.0	268.0
03	82.0	363.0	439.0	116.0
04	56.0	79.0	79.0	786.0
05	512.0	2.0	463.0	23.0
06	35.0	0.0	874.0	91.0
07	22.0	10.0	952.0	16.0
08	25.0	178.0	142.0	655.0
09	26.0	892.0	20.0	62.0
10	971.0	11.0	4.0	14.0
11	170.0	289.0	433.0	108.0
12	195.0	193.0	190.0	422.0
13	284.0	121.0	458.0	137.0
14	198.0	101.0	501.0	200.0
15	169.0	152.0	548.0	131.0

PFM

	A	C	G	T
01	0.611	0.25	0.049	0.09
02	0.681	0.02	0.031	0.268
03	0.082	0.363	0.439	0.116
04	0.056	0.079	0.079	0.786
05	0.512	0.002	0.463	0.023
06	0.035	0.0	0.874	0.091
07	0.022	0.01	0.952	0.016
08	0.025	0.178	0.142	0.655
09	0.026	0.892	0.02	0.062
10	0.971	0.011	0.004	0.014
11	0.17	0.289	0.433	0.108
12	0.195	0.193	0.19	0.422
13	0.284	0.121	0.458	0.137
14	0.198	0.101	0.501	0.2
15	0.169	0.152	0.548	0.131

PWM

	A	C	G	T
01	0.89	0.0	-1.602	-1.01
02	0.998	-2.45	-2.04	0.069
03	-1.101	0.371	0.56	-0.76
04	-1.473	-1.137	-1.137	1.141
05	0.713	-4.213	0.613	-2.32
06	-1.925	-4.982	1.247	-0.999
07	-2.362	-3.066	1.332	-2.653
08	-2.243	-0.337	-0.56	0.959
09	-2.206	1.267	-2.45	-1.374
10	1.352	-2.985	-3.783	-2.773
11	-0.382	0.144	0.546	-0.83
12	-0.247	-0.257	-0.272	0.521
13	0.127	-0.718	0.602	-0.596
14	-0.231	-0.896	0.692	-0.221
15	-0.388	-0.493	0.781	-0.64

Standard thresholds

P-value	Threshold
0.001	4.44446
0.0005	5.35711
0.0001	7.22261