RXRA.H14INVIVO.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRA.H14INVIVO.2.SM.B
Gene (human)	RXRA (GeneCards)
Gene synonyms (human)	NR2B1
Gene (mouse)	Rxra
Gene synonyms (mouse)	Nr2b1
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	15
Consensus	vdKKYYAAAGGTCAn
GC content	47.28%
Information content (bits; total / per base)	14.07 / 0.938
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9974
Previous names	RXRA.H12INVIVO.2.SM.B

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	9 (58)	0.771	0.84	0.648	0.721	0.719	0.796	2.074	2.445	67.724	129.796
Mouse	47 (263)	0.706	0.822	0.556	0.678	0.682	0.798	1.914	2.521	52.495	153.155

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 7 experiments	median	0.837	0.842	0.674	0.691	0.588	0.613
Overall, 7 experiments	best	1.0	1.0	0.955	0.957	0.777	0.805
Methyl HT-SELEX, 1 experiments	median	0.652	0.673	0.572	0.588	0.539	0.552
Methyl HT-SELEX, 1 experiments	best	0.652	0.673	0.572	0.588	0.539	0.552
Non-Methyl HT-SELEX, 6 experiments	median	0.875	0.878	0.7	0.717	0.602	0.629
Non-Methyl HT-SELEX, 6 experiments	best	1.0	1.0	0.955	0.957	0.777	0.805

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.067	2.349	0.139	0.101

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: 2.1.3.1.1
HGNC	HGNC:10477
MGI	MGI:98214
EntrezGene (human)	GeneID:6256 (SSTAR profile)
EntrezGene (mouse)	GeneID:20181 (SSTAR profile)
UniProt ID (human)	RXRA_HUMAN
UniProt ID (mouse)	RXRA_MOUSE
UniProt AC (human)	P19793 (TFClass)
UniProt AC (mouse)	P28700 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	9 human, 47 mouse
HT-SELEX	6
Methyl-HT-SELEX	1
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	RXRA.H14INVIVO.2.SM.B.pcm
PWM	RXRA.H14INVIVO.2.SM.B.pwm
PFM	RXRA.H14INVIVO.2.SM.B.pfm
Threshold to P-value map	RXRA.H14INVIVO.2.SM.B.thr
Motif in other formats
JASPAR format	RXRA.H14INVIVO.2.SM.B_jaspar_format.txt
MEME format	RXRA.H14INVIVO.2.SM.B_meme_format.meme
Transfac format	RXRA.H14INVIVO.2.SM.B_transfac_format.txt
Homer format	RXRA.H14INVIVO.2.SM.B_homer_format_0.001.txt RXRA.H14INVIVO.2.SM.B_homer_format_0.0005.txt RXRA.H14INVIVO.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3241.25	1429.25	3897.25	1406.25
02	4559.5	658.5	3970.5	785.5
03	787.0	621.0	7684.0	882.0
04	895.0	564.0	6553.0	1962.0
05	731.0	874.0	849.0	7520.0
06	999.0	6597.0	903.0	1475.0
07	8285.0	531.0	474.0	684.0
08	7963.0	196.0	1266.0	549.0
09	8631.0	57.0	1173.0	113.0
10	61.0	50.0	9764.0	99.0
11	105.0	64.0	8711.0	1094.0
12	144.0	86.0	270.0	9474.0
13	232.0	8213.0	493.0	1036.0
14	8566.25	154.25	1097.25	156.25
15	3332.0	2190.0	1347.0	3105.0

PFM

	A	C	G	T
01	0.325	0.143	0.391	0.141
02	0.457	0.066	0.398	0.079
03	0.079	0.062	0.77	0.088
04	0.09	0.057	0.657	0.197
05	0.073	0.088	0.085	0.754
06	0.1	0.661	0.091	0.148
07	0.831	0.053	0.048	0.069
08	0.798	0.02	0.127	0.055
09	0.865	0.006	0.118	0.011
10	0.006	0.005	0.979	0.01
11	0.011	0.006	0.873	0.11
12	0.014	0.009	0.027	0.95
13	0.023	0.823	0.049	0.104
14	0.859	0.015	0.11	0.016
15	0.334	0.22	0.135	0.311

PWM

	A	C	G	T
01	0.262	-0.556	0.446	-0.572
02	0.603	-1.329	0.465	-1.153
03	-1.151	-1.387	1.125	-1.038
04	-1.023	-1.483	0.966	-0.239
05	-1.225	-1.047	-1.076	1.103
06	-0.913	0.972	-1.014	-0.524
07	1.2	-1.543	-1.656	-1.291
08	1.16	-2.533	-0.677	-1.51
09	1.241	-3.74	-0.753	-3.075
10	-3.674	-3.865	1.364	-3.204
11	-3.147	-3.628	1.25	-0.823
12	-2.837	-3.342	-2.215	1.334
13	-2.366	1.191	-1.617	-0.877
14	1.233	-2.769	-0.82	-2.756
15	0.29	-0.13	-0.615	0.219

Standard thresholds

P-value	Threshold
0.001	3.48561
0.0005	4.53491
0.0001	6.74831