RARG.H12INVIVO.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARG.H12INVIVO.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	nhRAGGTCAhdvvvdbn
GC content	47.07%
Information content (bits; total / per base)	13.445 / 0.791
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9944

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)	0.709	0.788	0.522	0.604	0.689	0.751	1.763	1.967	43.036	72.076

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.91	0.889	0.749	0.749	0.63	0.651
Overall, 10 experiments	best	0.999	0.999	0.998	0.996	0.995	0.992
Methyl HT-SELEX, 2 experiments	median	0.984	0.972	0.977	0.963	0.963	0.946
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	0.856	0.84	0.691	0.7	0.593	0.617
Non-Methyl HT-SELEX, 8 experiments	best	0.999	0.999	0.998	0.996	0.995	0.992

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.991	0.412	0.954	0.367
batch 2	0.56	0.102	0.446	0.316

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.2.SM.B.pcm
PWM	RARG.H12INVIVO.2.SM.B.pwm
PFM	RARG.H12INVIVO.2.SM.B.pfm
Alignment	RARG.H12INVIVO.2.SM.B.words.tsv
Threshold to P-value map	RARG.H12INVIVO.2.SM.B.thr
Motif in other formats
JASPAR format	RARG.H12INVIVO.2.SM.B_jaspar_format.txt
MEME format	RARG.H12INVIVO.2.SM.B_meme_format.meme
Transfac format	RARG.H12INVIVO.2.SM.B_transfac_format.txt
Homer format	RARG.H12INVIVO.2.SM.B_homer_format_0.001.txt RARG.H12INVIVO.2.SM.B_homer_format_0.0005.txt RARG.H12INVIVO.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2952.5	2425.5	2077.5	2488.5
02	4881.5	1666.5	978.5	2417.5
03	6515.0	309.0	2178.0	942.0
04	9229.0	129.0	584.0	2.0
05	0.0	0.0	9943.0	1.0
06	0.0	0.0	9632.0	312.0
07	2.0	2.0	18.0	9922.0
08	1.0	9912.0	8.0	23.0
09	9869.0	1.0	69.0	5.0
10	3214.0	2296.0	422.0	4012.0
11	2680.0	1338.0	4494.0	1432.0
12	5108.0	1386.0	2074.0	1376.0
13	2459.0	2209.0	4038.0	1238.0
14	1949.0	2417.0	4481.0	1097.0
15	1456.0	1067.0	3110.0	4311.0
16	1227.75	3519.75	2673.75	2522.75
17	3483.25	1916.25	2198.25	2346.25

PFM

	A	C	G	T
01	0.297	0.244	0.209	0.25
02	0.491	0.168	0.098	0.243
03	0.655	0.031	0.219	0.095
04	0.928	0.013	0.059	0.0
05	0.0	0.0	1.0	0.0
06	0.0	0.0	0.969	0.031
07	0.0	0.0	0.002	0.998
08	0.0	0.997	0.001	0.002
09	0.992	0.0	0.007	0.001
10	0.323	0.231	0.042	0.403
11	0.27	0.135	0.452	0.144
12	0.514	0.139	0.209	0.138
13	0.247	0.222	0.406	0.124
14	0.196	0.243	0.451	0.11
15	0.146	0.107	0.313	0.434
16	0.123	0.354	0.269	0.254
17	0.35	0.193	0.221	0.236

PWM

	A	C	G	T
01	0.172	-0.025	-0.179	0.001
02	0.674	-0.399	-0.931	-0.028
03	0.963	-2.079	-0.132	-0.969
04	1.311	-2.942	-1.446	-6.36
05	-6.986	-6.986	1.385	-6.625
06	-6.986	-6.986	1.354	-2.069
07	-6.36	-6.36	-4.809	1.383
08	-6.625	1.382	-5.487	-4.589
09	1.378	-6.625	-3.552	-5.831
10	0.257	-0.079	-1.769	0.478
11	0.075	-0.619	0.592	-0.551
12	0.72	-0.584	-0.181	-0.591
13	-0.011	-0.118	0.485	-0.696
14	-0.243	-0.028	0.589	-0.817
15	-0.534	-0.845	0.224	0.55
16	-0.705	0.347	0.073	0.015
17	0.337	-0.26	-0.123	-0.058

Standard thresholds

P-value	Threshold
0.001	2.34251
0.0005	3.99456
0.0001	7.19666