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

Motif	RXRG.H12INVITRO.1.SM.B
Gene (human)	RXRG (GeneCards)
Gene synonyms (human)	NR2B3
Gene (mouse)	Rxrg
Gene synonyms (mouse)	Nr2b3
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	16
Consensus	vRGGTYAAAGGTYAnv
GC content	49.85%
Information content (bits; total / per base)	17.72 / 1.108
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	7694

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	3 (14)	0.678	0.865	0.549	0.736	0.618	0.826	1.787	2.707	27.27	126.357

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	1.0	0.999	0.997	0.997	0.895	0.903
Overall, 5 experiments	best	1.0	1.0	0.998	0.998	0.99	0.987
Methyl HT-SELEX, 1 experiments	median	0.999	0.999	0.998	0.997	0.99	0.987
Methyl HT-SELEX, 1 experiments	best	0.999	0.999	0.998	0.997	0.99	0.987
Non-Methyl HT-SELEX, 4 experiments	median	1.0	1.0	0.991	0.99	0.861	0.876
Non-Methyl HT-SELEX, 4 experiments	best	1.0	1.0	0.998	0.998	0.965	0.962

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.651	0.332	0.794	0.554

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: 2.1.3.1.3
HGNC	HGNC:10479
MGI	MGI:98216
EntrezGene (human)	GeneID:6258 (SSTAR profile)
EntrezGene (mouse)	GeneID:20183 (SSTAR profile)
UniProt ID (human)	RXRG_HUMAN
UniProt ID (mouse)	RXRG_MOUSE
UniProt AC (human)	P48443 (TFClass)
UniProt AC (mouse)	P28705 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 3 mouse
HT-SELEX	4
Methyl-HT-SELEX	1

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

PCM

	A	C	G	T
01	2677.25	1097.25	2905.25	1014.25
02	3859.75	441.75	3103.75	288.75
03	259.0	231.0	6896.0	308.0
04	180.0	160.0	6514.0	840.0
05	88.0	351.0	705.0	6550.0
06	221.0	6025.0	608.0	840.0
07	7351.0	74.0	188.0	81.0
08	6745.0	62.0	463.0	424.0
09	7023.0	13.0	654.0	4.0
10	6.0	12.0	7649.0	27.0
11	22.0	6.0	7390.0	276.0
12	13.0	63.0	339.0	7279.0
13	194.0	6132.0	475.0	893.0
14	6584.0	131.0	873.0	106.0
15	2329.25	2060.25	1020.25	2284.25
16	1995.5	1677.5	3048.5	972.5

PFM

	A	C	G	T
01	0.348	0.143	0.378	0.132
02	0.502	0.057	0.403	0.038
03	0.034	0.03	0.896	0.04
04	0.023	0.021	0.847	0.109
05	0.011	0.046	0.092	0.851
06	0.029	0.783	0.079	0.109
07	0.955	0.01	0.024	0.011
08	0.877	0.008	0.06	0.055
09	0.913	0.002	0.085	0.001
10	0.001	0.002	0.994	0.004
11	0.003	0.001	0.96	0.036
12	0.002	0.008	0.044	0.946
13	0.025	0.797	0.062	0.116
14	0.856	0.017	0.113	0.014
15	0.303	0.268	0.133	0.297
16	0.259	0.218	0.396	0.126

PWM

	A	C	G	T
01	0.33	-0.56	0.412	-0.639
02	0.696	-1.467	0.478	-1.89
03	-1.998	-2.111	1.276	-1.826
04	-2.358	-2.474	1.219	-0.827
05	-3.061	-1.696	-1.002	1.224
06	-2.155	1.141	-1.149	-0.827
07	1.34	-3.229	-2.315	-3.141
08	1.254	-3.4	-1.421	-1.508
09	1.294	-4.839	-1.077	-5.733
10	-5.454	-4.907	1.38	-4.188
11	-4.375	-5.454	1.345	-1.935
12	-4.839	-3.385	-1.73	1.33
13	-2.284	1.159	-1.395	-0.766
14	1.23	-2.671	-0.789	-2.879
15	0.191	0.069	-0.633	0.172
16	0.037	-0.137	0.46	-0.681

Standard thresholds

P-value	Threshold
0.001	1.40746
0.0005	2.76056
0.0001	5.58831