RARG.H12INVITRO.3.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARG.H12INVITRO.3.S.B
Gene (human)	RARG (GeneCards)
Gene synonyms (human)	NR1B3
Gene (mouse)	Rarg
Gene synonyms (mouse)	Nr1b3
LOGO
LOGO (reverse complement)
Motif subtype	3
Quality	B

Motif length	17
Consensus	vddKbWMWWRAGGTCAh
GC content	45.34%
Information content (bits; total / per base)	14.504 / 0.853
Data sources	HT-SELEX
Aligned words	2430

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)	0.604	0.644	0.424	0.463	0.563	0.606	1.336	1.574	11.444	23.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.89	0.874	0.738	0.737	0.626	0.645
Overall, 10 experiments	best	1.0	1.0	0.998	0.998	0.992	0.989
Methyl HT-SELEX, 2 experiments	median	0.978	0.964	0.965	0.948	0.942	0.921
Methyl HT-SELEX, 2 experiments	best	0.999	0.999	0.997	0.995	0.989	0.985
Non-Methyl HT-SELEX, 8 experiments	median	0.842	0.83	0.69	0.696	0.598	0.617
Non-Methyl HT-SELEX, 8 experiments	best	1.0	1.0	0.998	0.998	0.992	0.989

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.963	0.037	0.947	0.473
batch 2	0.571	0.074	0.462	0.341

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.H12INVITRO.3.S.B.pcm
PWM	RARG.H12INVITRO.3.S.B.pwm
PFM	RARG.H12INVITRO.3.S.B.pfm
Alignment	RARG.H12INVITRO.3.S.B.words.tsv
Threshold to P-value map	RARG.H12INVITRO.3.S.B.thr
Motif in other formats
JASPAR format	RARG.H12INVITRO.3.S.B_jaspar_format.txt
MEME format	RARG.H12INVITRO.3.S.B_meme_format.meme
Transfac format	RARG.H12INVITRO.3.S.B_transfac_format.txt
Homer format	RARG.H12INVITRO.3.S.B_homer_format_0.001.txt RARG.H12INVITRO.3.S.B_homer_format_0.0005.txt RARG.H12INVITRO.3.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1055.0	335.0	719.0	321.0
02	946.25	216.25	1036.25	231.25
03	1205.0	143.0	788.0	294.0
04	106.0	279.0	1597.0	448.0
05	272.0	440.0	1283.0	435.0
06	487.0	371.0	113.0	1459.0
07	471.0	1572.0	155.0	232.0
08	1588.0	301.0	236.0	305.0
09	1721.0	163.0	164.0	382.0
10	1785.0	53.0	486.0	106.0
11	2242.0	28.0	153.0	7.0
12	6.0	17.0	2405.0	2.0
13	1.0	20.0	2151.0	258.0
14	18.0	27.0	35.0	2350.0
15	22.0	2311.0	43.0	54.0
16	2114.5	90.5	146.5	78.5
17	755.0	617.0	235.0	823.0

PFM

	A	C	G	T
01	0.434	0.138	0.296	0.132
02	0.389	0.089	0.426	0.095
03	0.496	0.059	0.324	0.121
04	0.044	0.115	0.657	0.184
05	0.112	0.181	0.528	0.179
06	0.2	0.153	0.047	0.6
07	0.194	0.647	0.064	0.095
08	0.653	0.124	0.097	0.126
09	0.708	0.067	0.067	0.157
10	0.735	0.022	0.2	0.044
11	0.923	0.012	0.063	0.003
12	0.002	0.007	0.99	0.001
13	0.0	0.008	0.885	0.106
14	0.007	0.011	0.014	0.967
15	0.009	0.951	0.018	0.022
16	0.87	0.037	0.06	0.032
17	0.311	0.254	0.097	0.339

PWM

	A	C	G	T
01	0.551	-0.593	0.168	-0.635
02	0.442	-1.027	0.533	-0.961
03	0.683	-1.436	0.259	-0.722
04	-1.731	-0.774	0.965	-0.303
05	-0.8	-0.321	0.746	-0.333
06	-0.22	-0.491	-1.668	0.874
07	-0.254	0.949	-1.357	-0.957
08	0.959	-0.699	-0.94	-0.686
09	1.039	-1.307	-1.301	-0.462
10	1.076	-2.406	-0.222	-1.731
11	1.303	-3.013	-1.369	-4.221
12	-4.34	-3.471	1.374	-5.039
13	-5.331	-3.324	1.262	-0.852
14	-3.419	-3.047	-2.803	1.35
15	-3.237	1.334	-2.607	-2.388
16	1.245	-1.886	-1.412	-2.025
17	0.217	0.015	-0.945	0.303

Standard thresholds

P-value	Threshold
0.001	3.24281
0.0005	4.36676
0.0001	6.70111