RARG.H14INVITRO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARG.H14INVITRO.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	9
Consensus	ndRGGTCAn
GC content	52.91%
Information content (bits; total / per base)	9.642 / 1.071
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9745
Previous names	RARG.H12INVITRO.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)	0.726	0.813	0.586	0.668	0.689	0.771	1.704	1.901	62.495	101.854

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.936	0.915	0.787	0.783	0.658	0.676
Overall, 10 experiments	best	0.999	0.999	0.998	0.997	0.995	0.992
Methyl HT-SELEX, 2 experiments	median	0.982	0.968	0.975	0.959	0.961	0.943
Methyl HT-SELEX, 2 experiments	best	0.998	0.997	0.996	0.994	0.992	0.989
Non-Methyl HT-SELEX, 8 experiments	median	0.887	0.868	0.724	0.728	0.617	0.638
Non-Methyl HT-SELEX, 8 experiments	best	0.999	0.999	0.998	0.997	0.995	0.992

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.984	0.453	0.932	0.305
batch 2	0.558	0.099	0.499	0.296

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.H14INVITRO.1.PSM.A.pcm
PWM	RARG.H14INVITRO.1.PSM.A.pwm
PFM	RARG.H14INVITRO.1.PSM.A.pfm
Threshold to P-value map	RARG.H14INVITRO.1.PSM.A.thr
Motif in other formats
JASPAR format	RARG.H14INVITRO.1.PSM.A_jaspar_format.txt
MEME format	RARG.H14INVITRO.1.PSM.A_meme_format.meme
Transfac format	RARG.H14INVITRO.1.PSM.A_transfac_format.txt
Homer format	RARG.H14INVITRO.1.PSM.A_homer_format_0.001.txt RARG.H14INVITRO.1.PSM.A_homer_format_0.0005.txt RARG.H14INVITRO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3204.5	1965.5	2219.5	2355.5
02	3231.25	1161.25	4061.25	1291.25
03	5910.0	648.0	2821.0	366.0
04	0.0	4.0	9724.0	17.0
05	0.0	0.0	9236.0	509.0
06	1.0	1.0	7.0	9736.0
07	19.0	9308.0	333.0	85.0
08	8727.25	96.25	823.25	98.25
09	3117.25	2230.25	1769.25	2628.25

PFM

	A	C	G	T
01	0.329	0.202	0.228	0.242
02	0.332	0.119	0.417	0.133
03	0.606	0.066	0.289	0.038
04	0.0	0.0	0.998	0.002
05	0.0	0.0	0.948	0.052
06	0.0	0.0	0.001	0.999
07	0.002	0.955	0.034	0.009
08	0.896	0.01	0.084	0.01
09	0.32	0.229	0.182	0.27

PWM

	A	C	G	T
01	0.274	-0.214	-0.093	-0.034
02	0.282	-0.74	0.511	-0.634
03	0.886	-1.322	0.147	-1.89
04	-6.968	-5.959	1.383	-4.839
05	-6.968	-6.968	1.332	-1.562
06	-6.606	-6.606	-5.57	1.385
07	-4.741	1.34	-1.984	-3.33
08	1.275	-3.209	-1.083	-3.189
09	0.246	-0.088	-0.32	0.076

Standard thresholds

P-value	Threshold
0.001	4.956155
0.0005	5.943865
0.0001	7.71438