RARG.H12INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARG.H12INVIVO.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	hvAGGTCAb
GC content	57.83%
Information content (bits; total / per base)	10.186 / 1.132
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1000

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)	0.751	0.852	0.626	0.731	0.735	0.846	2.074	2.551	69.268	95.009

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.904	0.855	0.772	0.751	0.649	0.658
Overall, 10 experiments	best	0.988	0.978	0.988	0.977	0.984	0.972
Methyl HT-SELEX, 2 experiments	median	0.968	0.944	0.962	0.937	0.941	0.915
Methyl HT-SELEX, 2 experiments	best	0.984	0.972	0.984	0.97	0.979	0.964
Non-Methyl HT-SELEX, 8 experiments	median	0.853	0.801	0.719	0.7	0.617	0.625
Non-Methyl HT-SELEX, 8 experiments	best	0.988	0.978	0.988	0.977	0.984	0.972

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.985	0.131	0.97	0.55
batch 2	0.555	0.094	0.377	0.193

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

PCM	RARG.H12INVIVO.1.PSM.A.pcm
PWM	RARG.H12INVIVO.1.PSM.A.pwm
PFM	RARG.H12INVIVO.1.PSM.A.pfm
Alignment	RARG.H12INVIVO.1.PSM.A.words.tsv
Threshold to P-value map	RARG.H12INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	RARG.H12INVIVO.1.PSM.A_jaspar_format.txt
MEME format	RARG.H12INVIVO.1.PSM.A_meme_format.meme
Transfac format	RARG.H12INVIVO.1.PSM.A_transfac_format.txt
Homer format	RARG.H12INVIVO.1.PSM.A_homer_format_0.001.txt RARG.H12INVIVO.1.PSM.A_homer_format_0.0005.txt RARG.H12INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	147.0	540.0	138.0	175.0
02	383.0	297.0	228.0	92.0
03	740.0	2.0	256.0	2.0
04	3.0	2.0	979.0	16.0
05	4.0	2.0	910.0	84.0
06	14.0	51.0	64.0	871.0
07	6.0	972.0	19.0	3.0
08	996.0	1.0	2.0	1.0
09	51.0	324.0	418.0	207.0

PFM

	A	C	G	T
01	0.147	0.54	0.138	0.175
02	0.383	0.297	0.228	0.092
03	0.74	0.002	0.256	0.002
04	0.003	0.002	0.979	0.016
05	0.004	0.002	0.91	0.084
06	0.014	0.051	0.064	0.871
07	0.006	0.972	0.019	0.003
08	0.996	0.001	0.002	0.001
09	0.051	0.324	0.418	0.207

PWM

	A	C	G	T
01	-0.526	0.766	-0.589	-0.354
02	0.424	0.171	-0.091	-0.988
03	1.081	-4.213	0.024	-4.213
04	-3.975	-4.213	1.36	-2.653
05	-3.783	-4.213	1.287	-1.077
06	-2.773	-1.563	-1.343	1.243
07	-3.484	1.353	-2.497	-3.975
08	1.377	-4.525	-4.213	-4.525
09	-1.563	0.258	0.511	-0.187

Standard thresholds

P-value	Threshold
0.001	4.691085
0.0005	5.707145
0.0001	7.698345