RARG.H13RSNP.3.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARG.H13RSNP.3.S.B
Gene (human)	RARG (GeneCards)
Gene synonyms (human)	NR1B3
Gene (mouse)	Rarg
Gene synonyms (mouse)	Nr1b3
LOGO
LOGO (reverse complement)
Motif subtype	3
Quality	B

Motif length	18
Consensus	nvRGGTCAWRAGGTCAnd
GC content	47.42%
Information content (bits; total / per base)	20.853 / 1.159
Data sources	HT-SELEX
Aligned words	1019
Previous names	RARG.H12RSNP.3.S.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	5 (21)	0.596	0.641	0.412	0.444	0.554	0.606	1.35	1.685	10.42	27.131

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.867	0.856	0.714	0.717	0.613	0.631
Overall, 10 experiments	best	1.0	1.0	0.998	0.997	0.986	0.983
Methyl HT-SELEX, 2 experiments	median	0.976	0.963	0.959	0.941	0.924	0.904
Methyl HT-SELEX, 2 experiments	best	0.999	0.999	0.996	0.995	0.984	0.98
Non-Methyl HT-SELEX, 8 experiments	median	0.801	0.797	0.66	0.67	0.581	0.601
Non-Methyl HT-SELEX, 8 experiments	best	1.0	1.0	0.998	0.997	0.986	0.983

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.955	0.074	0.934	0.382
batch 2	0.615	0.114	0.488	0.341

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	Nuclear receptors with C4 zinc fingers {2.1} (TFClass)
TF family	Thyroid hormone receptor-related {2.1.2} (TFClass)
TF subfamily	RAR (NR1B) {2.1.2.1} (TFClass)
TFClass ID	TFClass: 2.1.2.1.3
HGNC	HGNC:9866
MGI	MGI:97858
EntrezGene (human)	GeneID:5916 (SSTAR profile)
EntrezGene (mouse)	GeneID:19411 (SSTAR profile)
UniProt ID (human)	RARG_HUMAN
UniProt ID (mouse)	RARG_MOUSE
UniProt AC (human)	P13631 (TFClass)
UniProt AC (mouse)	P18911 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 0 mouse
HT-SELEX	8
Methyl-HT-SELEX	2
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	RARG.H13RSNP.3.S.B.pcm
PWM	RARG.H13RSNP.3.S.B.pwm
PFM	RARG.H13RSNP.3.S.B.pfm
Threshold to P-value map	RARG.H13RSNP.3.S.B.thr
Motif in other formats
JASPAR format	RARG.H13RSNP.3.S.B_jaspar_format.txt
MEME format	RARG.H13RSNP.3.S.B_meme_format.meme
Transfac format	RARG.H13RSNP.3.S.B_transfac_format.txt
Homer format	RARG.H13RSNP.3.S.B_homer_format_0.001.txt RARG.H13RSNP.3.S.B_homer_format_0.0005.txt RARG.H13RSNP.3.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	273.5	300.5	173.5	271.5
02	313.25	100.25	506.25	99.25
03	746.0	55.0	209.0	9.0
04	0.0	0.0	1019.0	0.0
05	0.0	0.0	1006.0	13.0
06	0.0	0.0	0.0	1019.0
07	0.0	1015.0	1.0	3.0
08	1010.0	0.0	8.0	1.0
09	679.0	63.0	18.0	259.0
10	685.0	9.0	187.0	138.0
11	889.0	13.0	114.0	3.0
12	56.0	3.0	960.0	0.0
13	15.0	5.0	915.0	84.0
14	1.0	1.0	130.0	887.0
15	3.0	857.0	50.0	109.0
16	841.0	99.0	44.0	35.0
17	377.0	252.0	167.0	223.0
18	411.75	183.75	233.75	189.75

PFM

	A	C	G	T
01	0.268	0.295	0.17	0.266
02	0.307	0.098	0.497	0.097
03	0.732	0.054	0.205	0.009
04	0.0	0.0	1.0	0.0
05	0.0	0.0	0.987	0.013
06	0.0	0.0	0.0	1.0
07	0.0	0.996	0.001	0.003
08	0.991	0.0	0.008	0.001
09	0.666	0.062	0.018	0.254
10	0.672	0.009	0.184	0.135
11	0.872	0.013	0.112	0.003
12	0.055	0.003	0.942	0.0
13	0.015	0.005	0.898	0.082
14	0.001	0.001	0.128	0.87
15	0.003	0.841	0.049	0.107
16	0.825	0.097	0.043	0.034
17	0.37	0.247	0.164	0.219
18	0.404	0.18	0.229	0.186

PWM

	A	C	G	T
01	0.071	0.164	-0.381	0.063
02	0.205	-0.922	0.683	-0.932
03	1.07	-1.509	-0.196	-3.174
04	-4.998	-4.998	1.381	-4.998
05	-4.998	-4.998	1.368	-2.857
06	-4.998	-4.998	-4.998	1.381
07	-4.998	1.377	-4.542	-3.993
08	1.372	-4.998	-3.272	-4.542
09	0.976	-1.377	-2.565	0.016
10	0.985	-3.174	-0.307	-0.607
11	1.245	-2.857	-0.796	-3.993
12	-1.491	-3.993	1.322	-4.998
13	-2.73	-3.64	1.274	-1.096
14	-4.542	-4.542	-0.666	1.243
15	-3.993	1.208	-1.601	-0.84
16	1.19	-0.935	-1.724	-1.943
17	0.39	-0.011	-0.419	-0.132
18	0.478	-0.324	-0.085	-0.292

Standard thresholds

P-value	Threshold
0.001	-1.48939
0.0005	0.18811
0.0001	3.72181