RARG.H13CORE.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARG.H13CORE.1.PSM.A
Gene (human)	RARG (GeneCards)
Gene synonyms (human)	NR1B3
Gene (mouse)	Rarg
Gene synonyms (mouse)	Nr1b3
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	11
Consensus	ndAGGTCAnvn
GC content	51.95%
Information content (bits; total / per base)	10.315 / 0.938
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9843
Previous names	RARG.H12CORE.1.PSM.A

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)	0.739	0.839	0.576	0.682	0.709	0.806	1.884	2.219	63.041	112.155

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.918	0.887	0.792	0.775	0.671	0.678
Overall, 10 experiments	best	0.998	0.996	0.996	0.994	0.993	0.989
Methyl HT-SELEX, 2 experiments	median	0.985	0.974	0.978	0.965	0.966	0.949
Methyl HT-SELEX, 2 experiments	best	0.996	0.994	0.995	0.991	0.991	0.986
Non-Methyl HT-SELEX, 8 experiments	median	0.873	0.841	0.731	0.722	0.631	0.64
Non-Methyl HT-SELEX, 8 experiments	best	0.998	0.996	0.996	0.994	0.993	0.989

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.998	0.496	0.971	0.382
batch 2	0.563	0.114	0.449	0.273

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.H13CORE.1.PSM.A.pcm
PWM	RARG.H13CORE.1.PSM.A.pwm
PFM	RARG.H13CORE.1.PSM.A.pfm
Threshold to P-value map	RARG.H13CORE.1.PSM.A.thr
Motif in other formats
JASPAR format	RARG.H13CORE.1.PSM.A_jaspar_format.txt
MEME format	RARG.H13CORE.1.PSM.A_meme_format.meme
Transfac format	RARG.H13CORE.1.PSM.A_transfac_format.txt
Homer format	RARG.H13CORE.1.PSM.A_homer_format_0.001.txt RARG.H13CORE.1.PSM.A_homer_format_0.0005.txt RARG.H13CORE.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2365.5	2410.5	1792.5	3274.5
02	4762.5	1052.5	2403.5	1624.5
03	8140.0	376.0	1284.0	43.0
04	0.0	2.0	9835.0	6.0
05	0.0	0.0	9425.0	418.0
06	7.0	20.0	268.0	9548.0
07	5.0	9472.0	102.0	264.0
08	8224.0	7.0	1611.0	1.0
09	2306.0	3046.0	1348.0	3143.0
10	1623.5	1818.5	4847.5	1553.5
11	2388.0	2115.0	3009.0	2331.0

PFM

	A	C	G	T
01	0.24	0.245	0.182	0.333
02	0.484	0.107	0.244	0.165
03	0.827	0.038	0.13	0.004
04	0.0	0.0	0.999	0.001
05	0.0	0.0	0.958	0.042
06	0.001	0.002	0.027	0.97
07	0.001	0.962	0.01	0.027
08	0.836	0.001	0.164	0.0
09	0.234	0.309	0.137	0.319
10	0.165	0.185	0.492	0.158
11	0.243	0.215	0.306	0.237

PWM

	A	C	G	T
01	-0.039	-0.021	-0.317	0.285
02	0.66	-0.848	-0.024	-0.415
03	1.196	-1.873	-0.65	-3.996
04	-6.977	-6.351	1.385	-5.693
05	-6.977	-6.977	1.342	-1.768
06	-5.579	-4.705	-2.21	1.355
07	-5.821	1.347	-3.162	-2.225
08	1.206	-5.579	-0.423	-6.616
09	-0.065	0.213	-0.601	0.245
10	-0.415	-0.302	0.678	-0.459
11	-0.03	-0.151	0.201	-0.054

Standard thresholds

P-value	Threshold
0.001	4.708085
0.0005	5.794755
0.0001	7.703525