RXRB.H12INVIVO.2.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRB.H12INVIVO.2.PS.A
Gene (human)	RXRB (GeneCards)
Gene synonyms (human)	NR2B2
Gene (mouse)	Rxrb
Gene synonyms (mouse)	Nr2b2
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	A

Motif length	9
Consensus	hRAGGYCAv
GC content	50.69%
Information content (bits; total / per base)	9.916 / 1.102
Data sources	ChIP-Seq + HT-SELEX
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
Human	1 (7)	0.78	0.794	0.622	0.639	0.768	0.778	2.128	2.191	79.42	97.824

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.968	0.957	0.879	0.864	0.726	0.74
Overall, 3 experiments	best	0.979	0.971	0.912	0.897	0.774	0.779
Methyl HT-SELEX, 1 experiments	median	0.979	0.971	0.912	0.897	0.774	0.779
Methyl HT-SELEX, 1 experiments	best	0.979	0.971	0.912	0.897	0.774	0.779
Non-Methyl HT-SELEX, 2 experiments	median	0.808	0.797	0.722	0.718	0.628	0.64
Non-Methyl HT-SELEX, 2 experiments	best	0.968	0.957	0.879	0.864	0.726	0.74

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.56	0.018	0.584	0.333

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	Nuclear receptors with C4 zinc fingers {2.1} (TFClass)
TF family	RXR-related receptors {2.1.3} (TFClass)
TF subfamily	RXR (NR2B) {2.1.3.1} (TFClass)
TFClass ID	TFClass: 2.1.3.1.2
HGNC	HGNC:10478
MGI	MGI:98215
EntrezGene (human)	GeneID:6257 (SSTAR profile)
EntrezGene (mouse)	GeneID:20182 (SSTAR profile)
UniProt ID (human)	RXRB_HUMAN
UniProt ID (mouse)	RXRB_MOUSE
UniProt AC (human)	P28702 (TFClass)
UniProt AC (mouse)	P28704 (TFClass)
GRECO-DB-TF	yes

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

PCM	RXRB.H12INVIVO.2.PS.A.pcm
PWM	RXRB.H12INVIVO.2.PS.A.pwm
PFM	RXRB.H12INVIVO.2.PS.A.pfm
Alignment	RXRB.H12INVIVO.2.PS.A.words.tsv
Threshold to P-value map	RXRB.H12INVIVO.2.PS.A.thr
Motif in other formats
JASPAR format	RXRB.H12INVIVO.2.PS.A_jaspar_format.txt
MEME format	RXRB.H12INVIVO.2.PS.A_meme_format.meme
Transfac format	RXRB.H12INVIVO.2.PS.A_transfac_format.txt
Homer format	RXRB.H12INVIVO.2.PS.A_homer_format_0.001.txt RXRB.H12INVIVO.2.PS.A_homer_format_0.0005.txt RXRB.H12INVIVO.2.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	542.0	280.0	86.0	92.0
02	607.0	59.0	308.0	26.0
03	862.0	0.0	136.0	2.0
04	7.0	0.0	985.0	8.0
05	13.0	8.0	862.0	117.0
06	33.0	127.0	70.0	770.0
07	14.0	931.0	36.0	19.0
08	965.0	6.0	12.0	17.0
09	216.0	261.0	395.0	128.0

PFM

	A	C	G	T
01	0.542	0.28	0.086	0.092
02	0.607	0.059	0.308	0.026
03	0.862	0.0	0.136	0.002
04	0.007	0.0	0.985	0.008
05	0.013	0.008	0.862	0.117
06	0.033	0.127	0.07	0.77
07	0.014	0.931	0.036	0.019
08	0.965	0.006	0.012	0.017
09	0.216	0.261	0.395	0.128

PWM

	A	C	G	T
01	0.77	0.113	-1.054	-0.988
02	0.883	-1.422	0.207	-2.206
03	1.233	-4.982	-0.603	-4.213
04	-3.362	-4.982	1.366	-3.253
05	-2.839	-3.253	1.233	-0.752
06	-1.981	-0.671	-1.255	1.12
07	-2.773	1.31	-1.898	-2.497
08	1.346	-3.484	-2.909	-2.598
09	-0.145	0.043	0.455	-0.663

Standard thresholds

P-value	Threshold
0.001	4.813935
0.0005	5.59009
0.0001	7.33439