RXRB.H12RSNP.0.P.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRB.H12RSNP.0.P.C
Gene (human)	RXRB (GeneCards)
Gene synonyms (human)	NR2B2
Gene (mouse)	Rxrb
Gene synonyms (mouse)	Nr2b2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	C

Motif length	15
Consensus	ddRRdSARAGKYCAv
GC content	54.81%
Information content (bits; total / per base)	11.571 / 0.771
Data sources	ChIP-Seq
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)	0.786	0.805	0.666	0.693	0.771	0.783	2.513	2.585	77.886	91.215

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.975	0.972	0.839	0.838	0.697	0.716
Overall, 3 experiments	best	0.987	0.985	0.882	0.877	0.744	0.754
Methyl HT-SELEX, 1 experiments	median	0.987	0.985	0.882	0.877	0.744	0.754
Methyl HT-SELEX, 1 experiments	best	0.987	0.985	0.882	0.877	0.744	0.754
Non-Methyl HT-SELEX, 2 experiments	median	0.811	0.813	0.702	0.708	0.613	0.63
Non-Methyl HT-SELEX, 2 experiments	best	0.975	0.972	0.839	0.838	0.697	0.716

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.604	0.017	0.569	0.303

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.H12RSNP.0.P.C.pcm
PWM	RXRB.H12RSNP.0.P.C.pwm
PFM	RXRB.H12RSNP.0.P.C.pfm
Alignment	RXRB.H12RSNP.0.P.C.words.tsv
Threshold to P-value map	RXRB.H12RSNP.0.P.C.thr
Motif in other formats
JASPAR format	RXRB.H12RSNP.0.P.C_jaspar_format.txt
MEME format	RXRB.H12RSNP.0.P.C_meme_format.meme
Transfac format	RXRB.H12RSNP.0.P.C_transfac_format.txt
Homer format	RXRB.H12RSNP.0.P.C_homer_format_0.001.txt RXRB.H12RSNP.0.P.C_homer_format_0.0005.txt RXRB.H12RSNP.0.P.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	219.0	131.0	319.0	331.0
02	357.0	48.0	467.0	128.0
03	176.0	17.0	691.0	116.0
04	171.0	44.0	670.0	115.0
05	176.0	173.0	414.0	237.0
06	97.0	650.0	182.0	71.0
07	803.0	141.0	22.0	34.0
08	589.0	40.0	360.0	11.0
09	832.0	3.0	156.0	9.0
10	17.0	1.0	976.0	6.0
11	19.0	15.0	717.0	249.0
12	34.0	212.0	126.0	628.0
13	38.0	831.0	94.0	37.0
14	908.0	14.0	34.0	44.0
15	176.0	205.0	468.0	151.0

PFM

	A	C	G	T
01	0.219	0.131	0.319	0.331
02	0.357	0.048	0.467	0.128
03	0.176	0.017	0.691	0.116
04	0.171	0.044	0.67	0.115
05	0.176	0.173	0.414	0.237
06	0.097	0.65	0.182	0.071
07	0.803	0.141	0.022	0.034
08	0.589	0.04	0.36	0.011
09	0.832	0.003	0.156	0.009
10	0.017	0.001	0.976	0.006
11	0.019	0.015	0.717	0.249
12	0.034	0.212	0.126	0.628
13	0.038	0.831	0.094	0.037
14	0.908	0.014	0.034	0.044
15	0.176	0.205	0.468	0.151

PWM

	A	C	G	T
01	-0.131	-0.64	0.242	0.279
02	0.354	-1.622	0.622	-0.663
03	-0.348	-2.598	1.012	-0.76
04	-0.377	-1.706	0.982	-0.769
05	-0.348	-0.365	0.502	-0.053
06	-0.936	0.951	-0.315	-1.242
07	1.162	-0.567	-2.362	-1.952
08	0.853	-1.797	0.363	-2.985
09	1.198	-3.975	-0.467	-3.156
10	-2.598	-4.525	1.357	-3.484
11	-2.497	-2.711	1.049	-0.004
12	-1.952	-0.164	-0.678	0.917
13	-1.846	1.196	-0.967	-1.872
14	1.285	-2.773	-1.952	-1.706
15	-0.348	-0.197	0.624	-0.5

Standard thresholds

P-value	Threshold
0.001	4.35526
0.0005	5.27446
0.0001	7.16861