RXRB.H12CORE.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRB.H12CORE.1.SM.B
Gene (human)	RXRB (GeneCards)
Gene synonyms (human)	NR2B2
Gene (mouse)	Rxrb
Gene synonyms (mouse)	Nr2b2
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	17
Consensus	ndRGGKSAAAGGTCAnv
GC content	52.8%
Information content (bits; total / per base)	17.065 / 1.004
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9440

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)	0.772	0.794	0.64	0.672	0.75	0.767	2.218	2.315	66.538	83.114

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.989	0.988	0.864	0.863	0.72	0.738
Overall, 3 experiments	best	0.999	0.999	0.915	0.913	0.781	0.789
Methyl HT-SELEX, 1 experiments	median	0.999	0.999	0.915	0.913	0.781	0.789
Methyl HT-SELEX, 1 experiments	best	0.999	0.999	0.915	0.913	0.781	0.789
Non-Methyl HT-SELEX, 2 experiments	median	0.823	0.829	0.719	0.726	0.629	0.644
Non-Methyl HT-SELEX, 2 experiments	best	0.989	0.988	0.864	0.863	0.72	0.738

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.606	0.028	0.523	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.H12CORE.1.SM.B.pcm
PWM	RXRB.H12CORE.1.SM.B.pwm
PFM	RXRB.H12CORE.1.SM.B.pfm
Alignment	RXRB.H12CORE.1.SM.B.words.tsv
Threshold to P-value map	RXRB.H12CORE.1.SM.B.thr
Motif in other formats
JASPAR format	RXRB.H12CORE.1.SM.B_jaspar_format.txt
MEME format	RXRB.H12CORE.1.SM.B_meme_format.meme
Transfac format	RXRB.H12CORE.1.SM.B_transfac_format.txt
Homer format	RXRB.H12CORE.1.SM.B_homer_format_0.001.txt RXRB.H12CORE.1.SM.B_homer_format_0.0005.txt RXRB.H12CORE.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3047.75	1704.75	2463.75	2223.75
02	2597.25	750.25	5189.25	903.25
03	3669.0	394.0	5009.0	368.0
04	397.0	332.0	8305.0	406.0
05	344.0	342.0	7536.0	1218.0
06	315.0	792.0	835.0	7498.0
07	593.0	6844.0	1133.0	870.0
08	8203.0	342.0	521.0	374.0
09	7835.0	76.0	1196.0	333.0
10	8404.0	11.0	1017.0	8.0
11	10.0	1.0	9412.0	17.0
12	13.0	10.0	9123.0	294.0
13	27.0	40.0	288.0	9085.0
14	95.0	8360.0	433.0	552.0
15	7004.0	62.0	2332.0	42.0
16	2735.0	2659.0	1362.0	2684.0
17	2296.0	1429.0	4437.0	1278.0

PFM

	A	C	G	T
01	0.323	0.181	0.261	0.236
02	0.275	0.079	0.55	0.096
03	0.389	0.042	0.531	0.039
04	0.042	0.035	0.88	0.043
05	0.036	0.036	0.798	0.129
06	0.033	0.084	0.088	0.794
07	0.063	0.725	0.12	0.092
08	0.869	0.036	0.055	0.04
09	0.83	0.008	0.127	0.035
10	0.89	0.001	0.108	0.001
11	0.001	0.0	0.997	0.002
12	0.001	0.001	0.966	0.031
13	0.003	0.004	0.031	0.962
14	0.01	0.886	0.046	0.058
15	0.742	0.007	0.247	0.004
16	0.29	0.282	0.144	0.284
17	0.243	0.151	0.47	0.135

PWM

	A	C	G	T
01	0.256	-0.325	0.043	-0.059
02	0.096	-1.144	0.787	-0.959
03	0.441	-1.785	0.752	-1.853
04	-1.778	-1.955	1.258	-1.755
05	-1.92	-1.926	1.16	-0.661
06	-2.008	-1.09	-1.037	1.155
07	-1.378	1.064	-0.733	-0.996
08	1.245	-1.926	-1.507	-1.837
09	1.199	-3.407	-0.679	-1.952
10	1.269	-5.181	-0.841	-5.436
11	-5.259	-6.577	1.383	-4.808
12	-5.04	-5.259	1.351	-2.076
13	-4.39	-4.023	-2.097	1.347
14	-3.19	1.264	-1.691	-1.45
15	1.087	-3.604	-0.012	-3.977
16	0.147	0.119	-0.549	0.129
17	-0.027	-0.501	0.631	-0.613

Standard thresholds

P-value	Threshold
0.001	1.77121
0.0005	3.10741
0.0001	5.87201