RARG.H12RSNP.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARG.H12RSNP.0.P.B
Gene (human)	RARG (GeneCards)
Gene synonyms (human)	NR1B3
Gene (mouse)	Rarg
Gene synonyms (mouse)	Nr1b3
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	18
Consensus	bhvAGGTCAbnnhRhYYb
GC content	58.22%
Information content (bits; total / per base)	11.482 / 0.638
Data sources	ChIP-Seq
Aligned words	873

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	0.886	0.666	0.835	0.696	0.898	2.858	4.425	52.398	122.796

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.772	0.716	0.672	0.644	0.596	0.592
Overall, 10 experiments	best	0.974	0.957	0.966	0.944	0.946	0.92
Methyl HT-SELEX, 2 experiments	median	0.931	0.893	0.906	0.862	0.864	0.821
Methyl HT-SELEX, 2 experiments	best	0.955	0.925	0.942	0.907	0.917	0.878
Non-Methyl HT-SELEX, 8 experiments	median	0.718	0.669	0.628	0.608	0.569	0.568
Non-Methyl HT-SELEX, 8 experiments	best	0.974	0.957	0.966	0.944	0.946	0.92

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.911	0.025	0.924	0.473
batch 2	0.559	0.08	0.285	0.135

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.H12RSNP.0.P.B.pcm
PWM	RARG.H12RSNP.0.P.B.pwm
PFM	RARG.H12RSNP.0.P.B.pfm
Alignment	RARG.H12RSNP.0.P.B.words.tsv
Threshold to P-value map	RARG.H12RSNP.0.P.B.thr
Motif in other formats
JASPAR format	RARG.H12RSNP.0.P.B_jaspar_format.txt
MEME format	RARG.H12RSNP.0.P.B_meme_format.meme
Transfac format	RARG.H12RSNP.0.P.B_transfac_format.txt
Homer format	RARG.H12RSNP.0.P.B_homer_format_0.001.txt RARG.H12RSNP.0.P.B_homer_format_0.0005.txt RARG.H12RSNP.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	96.0	364.0	195.0	218.0
02	182.0	418.0	130.0	143.0
03	237.0	343.0	149.0	144.0
04	631.0	6.0	226.0	10.0
05	14.0	3.0	755.0	101.0
06	10.0	26.0	776.0	61.0
07	14.0	50.0	46.0	763.0
08	4.0	797.0	61.0	11.0
09	803.0	8.0	21.0	41.0
10	95.0	380.0	278.0	120.0
11	219.0	284.0	247.0	123.0
12	174.0	276.0	280.0	143.0
13	153.0	159.0	76.0	485.0
14	125.0	76.0	611.0	61.0
15	317.0	287.0	133.0	136.0
16	53.0	617.0	55.0	148.0
17	93.0	594.0	41.0	145.0
18	87.0	290.0	91.0	405.0

PFM

	A	C	G	T
01	0.11	0.417	0.223	0.25
02	0.208	0.479	0.149	0.164
03	0.271	0.393	0.171	0.165
04	0.723	0.007	0.259	0.011
05	0.016	0.003	0.865	0.116
06	0.011	0.03	0.889	0.07
07	0.016	0.057	0.053	0.874
08	0.005	0.913	0.07	0.013
09	0.92	0.009	0.024	0.047
10	0.109	0.435	0.318	0.137
11	0.251	0.325	0.283	0.141
12	0.199	0.316	0.321	0.164
13	0.175	0.182	0.087	0.556
14	0.143	0.087	0.7	0.07
15	0.363	0.329	0.152	0.156
16	0.061	0.707	0.063	0.17
17	0.107	0.68	0.047	0.166
18	0.1	0.332	0.104	0.464

PWM

	A	C	G	T
01	-0.812	0.508	-0.112	-0.001
02	-0.18	0.646	-0.513	-0.419
03	0.082	0.449	-0.378	-0.412
04	1.057	-3.353	0.035	-2.934
05	-2.64	-3.847	1.236	-0.762
06	-2.934	-2.072	1.263	-1.255
07	-2.64	-1.448	-1.529	1.246
08	-3.654	1.29	-1.255	-2.852
09	1.297	-3.122	-2.271	-1.639
10	-0.822	0.551	0.24	-0.592
11	0.003	0.262	0.123	-0.568
12	-0.225	0.233	0.247	-0.419
13	-0.352	-0.314	-1.041	0.794
14	-0.552	-1.041	1.024	-1.255
15	0.371	0.272	-0.49	-0.468
16	-1.392	1.034	-1.356	-0.385
17	-0.843	0.996	-1.639	-0.405
18	-0.908	0.282	-0.864	0.615

Standard thresholds

P-value	Threshold
0.001	4.38261
0.0005	5.28036
0.0001	7.14461