RXRG.H12RSNP.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRG.H12RSNP.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	18
Consensus	nnRAGGTCAAAGGTCAhv
GC content	48.7%
Information content (bits; total / per base)	25.044 / 1.391
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2245

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)	0.53	0.545	0.401	0.429	0.624	0.816	1.757	2.659	16.337	83.004

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.999	0.999	0.993	0.991	0.873	0.885
Overall, 5 experiments	best	1.0	1.0	0.997	0.996	0.986	0.983
Methyl HT-SELEX, 1 experiments	median	0.999	0.999	0.997	0.996	0.986	0.983
Methyl HT-SELEX, 1 experiments	best	0.999	0.999	0.997	0.996	0.986	0.983
Non-Methyl HT-SELEX, 4 experiments	median	1.0	0.999	0.984	0.983	0.841	0.859
Non-Methyl HT-SELEX, 4 experiments	best	1.0	1.0	0.996	0.996	0.935	0.932

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.715	0.466	0.742	0.572

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.H12RSNP.1.SM.B.pcm
PWM	RXRG.H12RSNP.1.SM.B.pwm
PFM	RXRG.H12RSNP.1.SM.B.pfm
Alignment	RXRG.H12RSNP.1.SM.B.words.tsv
Threshold to P-value map	RXRG.H12RSNP.1.SM.B.thr
Motif in other formats
JASPAR format	RXRG.H12RSNP.1.SM.B_jaspar_format.txt
MEME format	RXRG.H12RSNP.1.SM.B_meme_format.meme
Transfac format	RXRG.H12RSNP.1.SM.B_transfac_format.txt
Homer format	RXRG.H12RSNP.1.SM.B_homer_format_0.001.txt RXRG.H12RSNP.1.SM.B_homer_format_0.0005.txt RXRG.H12RSNP.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	460.5	718.5	550.5	515.5
02	685.75	671.75	308.75	578.75
03	579.0	130.0	1323.0	213.0
04	1483.0	0.0	762.0	0.0
05	0.0	0.0	2244.0	1.0
06	0.0	0.0	2240.0	5.0
07	0.0	0.0	0.0	2245.0
08	0.0	2171.0	1.0	73.0
09	2244.0	0.0	1.0	0.0
10	2196.0	0.0	14.0	35.0
11	2245.0	0.0	0.0	0.0
12	0.0	0.0	2245.0	0.0
13	0.0	0.0	2241.0	4.0
14	0.0	1.0	1.0	2243.0
15	0.0	2131.0	10.0	104.0
16	2187.0	5.0	53.0	0.0
17	674.0	553.0	131.0	887.0
18	789.5	370.5	801.5	283.5

PFM

	A	C	G	T
01	0.205	0.32	0.245	0.23
02	0.305	0.299	0.138	0.258
03	0.258	0.058	0.589	0.095
04	0.661	0.0	0.339	0.0
05	0.0	0.0	1.0	0.0
06	0.0	0.0	0.998	0.002
07	0.0	0.0	0.0	1.0
08	0.0	0.967	0.0	0.033
09	1.0	0.0	0.0	0.0
10	0.978	0.0	0.006	0.016
11	1.0	0.0	0.0	0.0
12	0.0	0.0	1.0	0.0
13	0.0	0.0	0.998	0.002
14	0.0	0.0	0.0	0.999
15	0.0	0.949	0.004	0.046
16	0.974	0.002	0.024	0.0
17	0.3	0.246	0.058	0.395
18	0.352	0.165	0.357	0.126

PWM

	A	C	G	T
01	-0.197	0.246	-0.019	-0.085
02	0.2	0.179	-0.595	0.031
03	0.031	-1.451	0.856	-0.963
04	0.97	-5.677	0.305	-5.677
05	-5.677	-5.677	1.383	-5.259
06	-5.677	-5.677	1.381	-4.398
07	-5.677	-5.677	-5.677	1.384
08	-5.677	1.35	-5.259	-2.017
09	1.383	-5.677	-5.259	-5.677
10	1.362	-5.677	-3.565	-2.725
11	1.384	-5.677	-5.677	-5.677
12	-5.677	-5.677	1.384	-5.677
13	-5.677	-5.677	1.382	-4.554
14	-5.677	-5.259	-5.259	1.383
15	-5.677	1.332	-3.855	-1.671
16	1.358	-4.398	-2.328	-5.677
17	0.182	-0.015	-1.444	0.456
18	0.34	-0.414	0.355	-0.68

Standard thresholds

P-value	Threshold
0.001	-9.31314
0.0005	-7.07049
0.0001	-2.19414