RARG.H12RSNP.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARG.H12RSNP.2.SM.B
Gene (human)	RARG (GeneCards)
Gene synonyms (human)	NR1B3
Gene (mouse)	Rarg
Gene synonyms (mouse)	Nr1b3
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	17
Consensus	nhRAGGTCAhdRvvdbn
GC content	46.07%
Information content (bits; total / per base)	14.859 / 0.874
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	7333

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)	0.707	0.783	0.513	0.596	0.668	0.734	1.717	1.921	33.432	56.347

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.907	0.887	0.745	0.745	0.626	0.648
Overall, 10 experiments	best	0.999	0.999	0.997	0.996	0.994	0.992
Methyl HT-SELEX, 2 experiments	median	0.984	0.972	0.977	0.962	0.962	0.945
Methyl HT-SELEX, 2 experiments	best	0.998	0.996	0.996	0.993	0.992	0.988
Non-Methyl HT-SELEX, 8 experiments	median	0.853	0.838	0.688	0.697	0.591	0.616
Non-Methyl HT-SELEX, 8 experiments	best	0.999	0.999	0.997	0.996	0.994	0.992

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.991	0.357	0.961	0.367
batch 2	0.562	0.103	0.454	0.319

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.2.SM.B.pcm
PWM	RARG.H12RSNP.2.SM.B.pwm
PFM	RARG.H12RSNP.2.SM.B.pfm
Alignment	RARG.H12RSNP.2.SM.B.words.tsv
Threshold to P-value map	RARG.H12RSNP.2.SM.B.thr
Motif in other formats
JASPAR format	RARG.H12RSNP.2.SM.B_jaspar_format.txt
MEME format	RARG.H12RSNP.2.SM.B_meme_format.meme
Transfac format	RARG.H12RSNP.2.SM.B_transfac_format.txt
Homer format	RARG.H12RSNP.2.SM.B_homer_format_0.001.txt RARG.H12RSNP.2.SM.B_homer_format_0.0005.txt RARG.H12RSNP.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2264.25	1755.25	1518.25	1795.25
02	4043.5	1046.5	571.5	1671.5
03	5364.0	131.0	1316.0	522.0
04	7094.0	32.0	207.0	0.0
05	0.0	0.0	7333.0	0.0
06	0.0	0.0	7244.0	89.0
07	1.0	1.0	7.0	7324.0
08	0.0	7324.0	3.0	6.0
09	7311.0	0.0	21.0	1.0
10	2447.0	1466.0	173.0	3247.0
11	2129.0	745.0	3526.0	933.0
12	4417.0	915.0	1275.0	726.0
13	1733.0	1671.0	3298.0	631.0
14	1218.0	1884.0	3559.0	672.0
15	768.0	653.0	2240.0	3672.0
16	748.0	2943.0	1791.0	1851.0
17	2918.75	1325.75	1455.75	1632.75

PFM

	A	C	G	T
01	0.309	0.239	0.207	0.245
02	0.551	0.143	0.078	0.228
03	0.731	0.018	0.179	0.071
04	0.967	0.004	0.028	0.0
05	0.0	0.0	1.0	0.0
06	0.0	0.0	0.988	0.012
07	0.0	0.0	0.001	0.999
08	0.0	0.999	0.0	0.001
09	0.997	0.0	0.003	0.0
10	0.334	0.2	0.024	0.443
11	0.29	0.102	0.481	0.127
12	0.602	0.125	0.174	0.099
13	0.236	0.228	0.45	0.086
14	0.166	0.257	0.485	0.092
15	0.105	0.089	0.305	0.501
16	0.102	0.401	0.244	0.252
17	0.398	0.181	0.199	0.223

PWM

	A	C	G	T
01	0.211	-0.043	-0.188	-0.021
02	0.79	-0.56	-1.163	-0.092
03	1.073	-2.623	-0.331	-1.253
04	1.352	-3.982	-2.172	-6.715
05	-6.715	-6.715	1.385	-6.715
06	-6.715	-6.715	1.373	-3.002
07	-6.344	-6.344	-5.293	1.384
08	-6.715	1.384	-5.862	-5.408
09	1.382	-6.715	-4.37	-6.344
10	0.288	-0.223	-2.349	0.571
11	0.149	-0.899	0.653	-0.674
12	0.879	-0.694	-0.363	-0.924
13	-0.056	-0.093	0.587	-1.064
14	-0.408	0.027	0.663	-1.001
15	-0.868	-1.03	0.2	0.694
16	-0.895	0.473	-0.023	0.01
17	0.465	-0.324	-0.23	-0.116

Standard thresholds

P-value	Threshold
0.001	1.23786
0.0005	2.85221
0.0001	6.51036