RXRG.H12INVIVO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRG.H12INVIVO.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	vRGKKYARAGGTCAnv
GC content	50.82%
Information content (bits; total / per base)	15.032 / 0.939
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9949

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)	0.693	0.901	0.574	0.792	0.633	0.87	1.914	3.066	33.965	139.432

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.999	0.999	0.997	0.996	0.904	0.911
Overall, 5 experiments	best	1.0	1.0	0.998	0.998	0.99	0.986
Methyl HT-SELEX, 1 experiments	median	0.999	0.999	0.997	0.996	0.99	0.986
Methyl HT-SELEX, 1 experiments	best	0.999	0.999	0.997	0.996	0.99	0.986
Non-Methyl HT-SELEX, 4 experiments	median	1.0	1.0	0.992	0.991	0.871	0.883
Non-Methyl HT-SELEX, 4 experiments	best	1.0	1.0	0.998	0.998	0.969	0.965

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.661	0.333	0.783	0.533

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.H12INVIVO.1.SM.B.pcm
PWM	RXRG.H12INVIVO.1.SM.B.pwm
PFM	RXRG.H12INVIVO.1.SM.B.pfm
Alignment	RXRG.H12INVIVO.1.SM.B.words.tsv
Threshold to P-value map	RXRG.H12INVIVO.1.SM.B.thr
Motif in other formats
JASPAR format	RXRG.H12INVIVO.1.SM.B_jaspar_format.txt
MEME format	RXRG.H12INVIVO.1.SM.B_meme_format.meme
Transfac format	RXRG.H12INVIVO.1.SM.B_transfac_format.txt
Homer format	RXRG.H12INVIVO.1.SM.B_homer_format_0.001.txt RXRG.H12INVIVO.1.SM.B_homer_format_0.0005.txt RXRG.H12INVIVO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3315.75	1540.75	3693.75	1398.75
02	4456.75	823.75	4106.75	561.75
03	618.0	588.0	8126.0	617.0
04	475.0	543.0	7436.0	1495.0
05	313.0	1042.0	1268.0	7326.0
06	823.0	6709.0	1092.0	1325.0
07	8515.0	504.0	445.0	485.0
08	7837.0	177.0	1272.0	663.0
09	8555.0	31.0	1355.0	8.0
10	9.0	30.0	9868.0	42.0
11	45.0	12.0	9476.0	416.0
12	26.0	83.0	481.0	9359.0
13	251.0	7948.0	630.0	1120.0
14	8470.0	186.0	1158.0	135.0
15	2946.75	2743.75	1259.75	2998.75
16	2517.75	2109.75	4151.75	1169.75

PFM

	A	C	G	T
01	0.333	0.155	0.371	0.141
02	0.448	0.083	0.413	0.056
03	0.062	0.059	0.817	0.062
04	0.048	0.055	0.747	0.15
05	0.031	0.105	0.127	0.736
06	0.083	0.674	0.11	0.133
07	0.856	0.051	0.045	0.049
08	0.788	0.018	0.128	0.067
09	0.86	0.003	0.136	0.001
10	0.001	0.003	0.992	0.004
11	0.005	0.001	0.952	0.042
12	0.003	0.008	0.048	0.941
13	0.025	0.799	0.063	0.113
14	0.851	0.019	0.116	0.014
15	0.296	0.276	0.127	0.301
16	0.253	0.212	0.417	0.118

PWM

	A	C	G	T
01	0.287	-0.478	0.395	-0.575
02	0.583	-1.103	0.501	-1.485
03	-1.39	-1.439	1.183	-1.391
04	-1.652	-1.519	1.095	-0.508
05	-2.066	-0.869	-0.673	1.08
06	-1.104	0.992	-0.822	-0.629
07	1.23	-1.593	-1.717	-1.631
08	1.147	-2.631	-0.67	-1.32
09	1.235	-4.314	-0.607	-5.488
10	-5.395	-4.345	1.377	-4.029
11	-3.963	-5.16	1.337	-1.784
12	-4.477	-3.374	-1.639	1.324
13	-2.285	1.161	-1.37	-0.797
14	1.225	-2.582	-0.763	-2.898
15	0.169	0.098	-0.679	0.187
16	0.012	-0.164	0.512	-0.753

Standard thresholds

P-value	Threshold
0.001	2.98826
0.0005	4.15031
0.0001	6.55081