RARB.H12INVIVO.1.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARB.H12INVIVO.1.P.B
Gene (human)	RARB (GeneCards)
Gene synonyms (human)	HAP, NR1B2
Gene (mouse)	Rarb
Gene synonyms (mouse)	Nr1b2
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	12
Consensus	vWdRGKbCARdR
GC content	55.36%
Information content (bits; total / per base)	8.624 / 0.719
Data sources	ChIP-Seq
Aligned words	1028

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	2 (14)	0.621	0.664	0.45	0.506	0.608	0.646	1.47	1.681	15.353	32.721

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.743	0.695	0.65	0.629	0.578	0.58
Overall, 2 experiments	best	0.808	0.752	0.706	0.674	0.615	0.612
Methyl HT-SELEX, 1 experiments	median	0.808	0.752	0.706	0.674	0.615	0.612
Methyl HT-SELEX, 1 experiments	best	0.808	0.752	0.706	0.674	0.615	0.612
Non-Methyl HT-SELEX, 1 experiments	median	0.678	0.639	0.593	0.583	0.541	0.548
Non-Methyl HT-SELEX, 1 experiments	best	0.678	0.639	0.593	0.583	0.541	0.548

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	RAR (NR1B) {2.1.2.1} (TFClass)
TFClass ID	TFClass: 2.1.2.1.2
HGNC	HGNC:9865
MGI	MGI:97857
EntrezGene (human)	GeneID:5915 (SSTAR profile)
EntrezGene (mouse)	GeneID:218772 (SSTAR profile)
UniProt ID (human)	RARB_HUMAN
UniProt ID (mouse)	RARB_MOUSE
UniProt AC (human)	P10826 (TFClass)
UniProt AC (mouse)	P22605 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 2 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	RARB.H12INVIVO.1.P.B.pcm
PWM	RARB.H12INVIVO.1.P.B.pwm
PFM	RARB.H12INVIVO.1.P.B.pfm
Alignment	RARB.H12INVIVO.1.P.B.words.tsv
Threshold to P-value map	RARB.H12INVIVO.1.P.B.thr
Motif in other formats
JASPAR format	RARB.H12INVIVO.1.P.B_jaspar_format.txt
MEME format	RARB.H12INVIVO.1.P.B_meme_format.meme
Transfac format	RARB.H12INVIVO.1.P.B_transfac_format.txt
Homer format	RARB.H12INVIVO.1.P.B_homer_format_0.001.txt RARB.H12INVIVO.1.P.B_homer_format_0.0005.txt RARB.H12INVIVO.1.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	179.0	475.0	267.0	107.0
02	628.0	119.0	135.0	146.0
03	367.0	89.0	475.0	97.0
04	683.0	7.0	242.0	96.0
05	18.0	12.0	969.0	29.0
06	50.0	45.0	698.0	235.0
07	132.0	217.0	198.0	481.0
08	18.0	946.0	49.0	15.0
09	960.0	12.0	45.0	11.0
10	407.0	68.0	494.0	59.0
11	405.0	76.0	445.0	102.0
12	191.0	73.0	673.0	91.0

PFM

	A	C	G	T
01	0.174	0.462	0.26	0.104
02	0.611	0.116	0.131	0.142
03	0.357	0.087	0.462	0.094
04	0.664	0.007	0.235	0.093
05	0.018	0.012	0.943	0.028
06	0.049	0.044	0.679	0.229
07	0.128	0.211	0.193	0.468
08	0.018	0.92	0.048	0.015
09	0.934	0.012	0.044	0.011
10	0.396	0.066	0.481	0.057
11	0.394	0.074	0.433	0.099
12	0.186	0.071	0.655	0.089

PWM

	A	C	G	T
01	-0.359	0.611	0.038	-0.867
02	0.889	-0.762	-0.638	-0.56
03	0.354	-1.048	0.611	-0.963
04	0.973	-3.389	-0.06	-0.974
05	-2.573	-2.936	1.322	-2.13
06	-1.61	-1.711	0.995	-0.089
07	-0.66	-0.168	-0.259	0.624
08	-2.573	1.298	-1.629	-2.738
09	1.313	-2.936	-1.711	-3.012
10	0.457	-1.311	0.65	-1.449
11	0.452	-1.203	0.546	-0.914
12	-0.294	-1.242	0.959	-1.026

Standard thresholds

P-value	Threshold
0.001	4.966215
0.0005	5.701215
0.0001	7.17091