NR1D1.H12INVITRO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1D1.H12INVITRO.1.SM.B
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	B

Motif length	18
Consensus	dbKRGGTYAGTRGGTSRn
GC content	54.12%
Information content (bits; total / per base)	19.238 / 1.069
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2649

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)	0.673	0.756	0.568	0.669	0.681	0.762	2.473	3.808	45.481	131.444

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.885	0.887	0.727	0.735	0.635	0.649
Overall, 2 experiments	best	0.95	0.951	0.776	0.784	0.681	0.688
Methyl HT-SELEX, 1 experiments	median	0.95	0.951	0.776	0.784	0.681	0.688
Methyl HT-SELEX, 1 experiments	best	0.95	0.951	0.776	0.784	0.681	0.688
Non-Methyl HT-SELEX, 1 experiments	median	0.821	0.823	0.677	0.687	0.588	0.61
Non-Methyl HT-SELEX, 1 experiments	best	0.821	0.823	0.677	0.687	0.588	0.61

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.1.SM.B.pcm
PWM	NR1D1.H12INVITRO.1.SM.B.pwm
PFM	NR1D1.H12INVITRO.1.SM.B.pfm
Alignment	NR1D1.H12INVITRO.1.SM.B.words.tsv
Threshold to P-value map	NR1D1.H12INVITRO.1.SM.B.thr
Motif in other formats
JASPAR format	NR1D1.H12INVITRO.1.SM.B_jaspar_format.txt
MEME format	NR1D1.H12INVITRO.1.SM.B_meme_format.meme
Transfac format	NR1D1.H12INVITRO.1.SM.B_transfac_format.txt
Homer format	NR1D1.H12INVITRO.1.SM.B_homer_format_0.001.txt NR1D1.H12INVITRO.1.SM.B_homer_format_0.0005.txt NR1D1.H12INVITRO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1082.75	135.75	323.75	1106.75
02	400.0	471.0	1219.0	559.0
03	96.0	368.0	401.0	1784.0
04	1335.0	34.0	1255.0	25.0
05	1.0	2.0	2596.0	50.0
06	1.0	0.0	2646.0	2.0
07	63.0	7.0	66.0	2513.0
08	4.0	1606.0	480.0	559.0
09	2153.0	3.0	492.0	1.0
10	137.0	294.0	2135.0	83.0
11	65.0	51.0	162.0	2371.0
12	1385.0	9.0	1238.0	17.0
13	2.0	7.0	2541.0	99.0
14	12.0	5.0	2608.0	24.0
15	69.0	79.0	402.0	2099.0
16	58.0	2046.0	279.0	266.0
17	2024.25	44.25	471.25	109.25
18	647.5	545.5	784.5	671.5

PFM

	A	C	G	T
01	0.409	0.051	0.122	0.418
02	0.151	0.178	0.46	0.211
03	0.036	0.139	0.151	0.673
04	0.504	0.013	0.474	0.009
05	0.0	0.001	0.98	0.019
06	0.0	0.0	0.999	0.001
07	0.024	0.003	0.025	0.949
08	0.002	0.606	0.181	0.211
09	0.813	0.001	0.186	0.0
10	0.052	0.111	0.806	0.031
11	0.025	0.019	0.061	0.895
12	0.523	0.003	0.467	0.006
13	0.001	0.003	0.959	0.037
14	0.005	0.002	0.985	0.009
15	0.026	0.03	0.152	0.792
16	0.022	0.772	0.105	0.1
17	0.764	0.017	0.178	0.041
18	0.244	0.206	0.296	0.253

PWM

	A	C	G	T
01	0.49	-1.573	-0.713	0.512
02	-0.502	-0.34	0.609	-0.169
03	-1.914	-0.585	-0.5	0.989
04	0.7	-2.916	0.638	-3.204
05	-5.41	-5.12	1.364	-2.548
06	-5.41	-5.82	1.383	-5.12
07	-2.325	-4.305	-2.28	1.331
08	-4.712	0.884	-0.321	-0.169
09	1.177	-4.895	-0.296	-5.41
10	-1.564	-0.808	1.169	-2.056
11	-2.294	-2.529	-1.399	1.273
12	0.736	-4.103	0.624	-3.556
13	-5.12	-4.305	1.342	-1.884
14	-3.862	-4.557	1.368	-3.242
15	-2.236	-2.105	-0.497	1.152
16	-2.405	1.126	-0.86	-0.908
17	1.115	-2.665	-0.339	-1.787
18	-0.022	-0.193	0.169	0.014

Standard thresholds

P-value	Threshold
0.001	0.00571
0.0005	1.54556
0.0001	4.76181