RARB.H12INVIVO.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARB.H12INVIVO.0.SM.B
Gene (human)	RARB (GeneCards)
Gene synonyms (human)	HAP, NR1B2
Gene (mouse)	Rarb
Gene synonyms (mouse)	Nr1b2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	10
Consensus	dRAGGTCAhb
GC content	50.79%
Information content (bits; total / per base)	10.7 / 1.07
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9967

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)	0.636	0.661	0.458	0.508	0.581	0.615	1.364	1.554	16.393	32.602

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.863	0.842	0.728	0.724	0.623	0.638
Overall, 2 experiments	best	0.936	0.915	0.804	0.793	0.668	0.684
Methyl HT-SELEX, 1 experiments	median	0.936	0.915	0.804	0.793	0.668	0.684
Methyl HT-SELEX, 1 experiments	best	0.936	0.915	0.804	0.793	0.668	0.684
Non-Methyl HT-SELEX, 1 experiments	median	0.79	0.768	0.652	0.654	0.577	0.592
Non-Methyl HT-SELEX, 1 experiments	best	0.79	0.768	0.652	0.654	0.577	0.592

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.0.SM.B.pcm
PWM	RARB.H12INVIVO.0.SM.B.pwm
PFM	RARB.H12INVIVO.0.SM.B.pfm
Alignment	RARB.H12INVIVO.0.SM.B.words.tsv
Threshold to P-value map	RARB.H12INVIVO.0.SM.B.thr
Motif in other formats
JASPAR format	RARB.H12INVIVO.0.SM.B_jaspar_format.txt
MEME format	RARB.H12INVIVO.0.SM.B_meme_format.meme
Transfac format	RARB.H12INVIVO.0.SM.B_transfac_format.txt
Homer format	RARB.H12INVIVO.0.SM.B_homer_format_0.001.txt RARB.H12INVIVO.0.SM.B_homer_format_0.0005.txt RARB.H12INVIVO.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	4003.5	1761.5	1914.5	2287.5
02	5588.75	563.75	2933.75	880.75
03	8431.0	119.0	1290.0	127.0
04	0.0	7.0	9945.0	15.0
05	1.0	0.0	9689.0	277.0
06	5.0	4.0	69.0	9889.0
07	51.0	9668.0	168.0	80.0
08	8118.0	92.0	1685.0	72.0
09	2580.0	3458.0	1114.0	2815.0
10	1913.75	1972.75	4164.75	1915.75

PFM

	A	C	G	T
01	0.402	0.177	0.192	0.23
02	0.561	0.057	0.294	0.088
03	0.846	0.012	0.129	0.013
04	0.0	0.001	0.998	0.002
05	0.0	0.0	0.972	0.028
06	0.001	0.0	0.007	0.992
07	0.005	0.97	0.017	0.008
08	0.814	0.009	0.169	0.007
09	0.259	0.347	0.112	0.282
10	0.192	0.198	0.418	0.192

PWM

	A	C	G	T
01	0.474	-0.346	-0.263	-0.085
02	0.807	-1.483	0.163	-1.038
03	1.218	-3.023	-0.657	-2.96
04	-6.988	-5.591	1.383	-4.971
05	-6.627	-6.988	1.357	-2.189
06	-5.834	-5.981	-3.555	1.378
07	-3.846	1.355	-2.684	-3.411
08	1.18	-3.275	-0.391	-3.514
09	0.035	0.327	-0.804	0.122
10	-0.264	-0.233	0.513	-0.263

Standard thresholds

P-value	Threshold
0.001	4.344235
0.0005	5.590775
0.0001	7.682985