RARG.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARG.H12INVIVO.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	bhvAGGTCAvnvhRvYYb
GC content	58.41%
Information content (bits; total / per base)	12.019 / 0.668
Data sources	ChIP-Seq
Aligned words	920

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)	0.749	0.895	0.677	0.843	0.702	0.902	2.841	4.419	61.409	128.854

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.786	0.729	0.681	0.654	0.601	0.598
Overall, 10 experiments	best	0.975	0.959	0.969	0.948	0.953	0.929
Methyl HT-SELEX, 2 experiments	median	0.939	0.903	0.917	0.876	0.879	0.838
Methyl HT-SELEX, 2 experiments	best	0.961	0.934	0.951	0.919	0.93	0.895
Non-Methyl HT-SELEX, 8 experiments	median	0.731	0.681	0.636	0.616	0.573	0.572
Non-Methyl HT-SELEX, 8 experiments	best	0.975	0.959	0.969	0.948	0.953	0.929

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.88	0.026	0.911	0.458
batch 2	0.532	0.077	0.297	0.138

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.0.P.B.pcm
PWM	RARG.H12INVIVO.0.P.B.pwm
PFM	RARG.H12INVIVO.0.P.B.pfm
Alignment	RARG.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	RARG.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	RARG.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	RARG.H12INVIVO.0.P.B_meme_format.meme
Transfac format	RARG.H12INVIVO.0.P.B_transfac_format.txt
Homer format	RARG.H12INVIVO.0.P.B_homer_format_0.001.txt RARG.H12INVIVO.0.P.B_homer_format_0.0005.txt RARG.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	111.0	355.0	219.0	235.0
02	169.0	429.0	152.0	170.0
03	251.0	383.0	155.0	131.0
04	700.0	11.0	200.0	9.0
05	5.0	1.0	816.0	98.0
06	17.0	13.0	843.0	47.0
07	22.0	4.0	105.0	789.0
08	0.0	853.0	59.0	8.0
09	884.0	11.0	15.0	10.0
10	123.0	332.0	352.0	113.0
11	232.0	285.0	289.0	114.0
12	178.0	290.0	324.0	128.0
13	176.0	158.0	62.0	524.0
14	139.0	89.0	640.0	52.0
15	363.0	266.0	149.0	142.0
16	66.0	650.0	71.0	133.0
17	101.0	606.0	34.0	179.0
18	94.0	343.0	109.0	374.0

PFM

	A	C	G	T
01	0.121	0.386	0.238	0.255
02	0.184	0.466	0.165	0.185
03	0.273	0.416	0.168	0.142
04	0.761	0.012	0.217	0.01
05	0.005	0.001	0.887	0.107
06	0.018	0.014	0.916	0.051
07	0.024	0.004	0.114	0.858
08	0.0	0.927	0.064	0.009
09	0.961	0.012	0.016	0.011
10	0.134	0.361	0.383	0.123
11	0.252	0.31	0.314	0.124
12	0.193	0.315	0.352	0.139
13	0.191	0.172	0.067	0.57
14	0.151	0.097	0.696	0.057
15	0.395	0.289	0.162	0.154
16	0.072	0.707	0.077	0.145
17	0.11	0.659	0.037	0.195
18	0.102	0.373	0.118	0.407

PWM

	A	C	G	T
01	-0.721	0.431	-0.049	0.021
02	-0.306	0.62	-0.41	-0.3
03	0.087	0.507	-0.391	-0.557
04	1.108	-2.903	-0.139	-3.075
05	-3.542	-4.45	1.261	-0.843
06	-2.517	-2.757	1.294	-1.56
07	-2.28	-3.704	-0.775	1.227
08	-4.911	1.305	-1.339	-3.173
09	1.341	-2.903	-2.63	-2.985
10	-0.62	0.365	0.423	-0.703
11	0.009	0.213	0.227	-0.694
12	-0.254	0.23	0.341	-0.58
13	-0.265	-0.372	-1.291	0.819
14	-0.499	-0.938	1.019	-1.462
15	0.454	0.144	-0.43	-0.478
16	-1.23	1.034	-1.159	-0.542
17	-0.814	0.964	-1.87	-0.249
18	-0.884	0.397	-0.739	0.483

Standard thresholds

P-value	Threshold
0.001	4.22096
0.0005	5.18011
0.0001	7.15276