RXRA.H12RSNP.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRA.H12RSNP.0.PS.A
Gene (human)	RXRA (GeneCards)
Gene synonyms (human)	NR2B1
Gene (mouse)	Rxra
Gene synonyms (mouse)	Nr2b1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	9
Consensus	nhRAGGTCA
GC content	53.64%
Information content (bits; total / per base)	9.938 / 1.104
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1000

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	9 (58)	0.747	0.824	0.575	0.66	0.728	0.809	1.949	2.318	84.901	178.0
Mouse	47 (263)	0.78	0.875	0.638	0.766	0.742	0.872	2.026	2.693	79.292	222.102

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 7 experiments	median	0.885	0.854	0.733	0.736	0.616	0.642
Overall, 7 experiments	best	0.997	0.993	0.959	0.954	0.781	0.806
Methyl HT-SELEX, 1 experiments	median	0.658	0.648	0.58	0.582	0.541	0.548
Methyl HT-SELEX, 1 experiments	best	0.658	0.648	0.58	0.582	0.541	0.548
Non-Methyl HT-SELEX, 6 experiments	median	0.896	0.872	0.742	0.738	0.628	0.645
Non-Methyl HT-SELEX, 6 experiments	best	0.997	0.993	0.959	0.954	0.781	0.806

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	8.944	6.261	0.199	0.125

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	Nuclear receptors with C4 zinc fingers {2.1} (TFClass)
TF family	RXR-related receptors {2.1.3} (TFClass)
TF subfamily	RXR (NR2B) {2.1.3.1} (TFClass)
TFClass ID	TFClass: 2.1.3.1.1
HGNC	HGNC:10477
MGI	MGI:98214
EntrezGene (human)	GeneID:6256 (SSTAR profile)
EntrezGene (mouse)	GeneID:20181 (SSTAR profile)
UniProt ID (human)	RXRA_HUMAN
UniProt ID (mouse)	RXRA_MOUSE
UniProt AC (human)	P19793 (TFClass)
UniProt AC (mouse)	P28700 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	9 human, 47 mouse
HT-SELEX	6
Methyl-HT-SELEX	1

PCM	RXRA.H12RSNP.0.PS.A.pcm
PWM	RXRA.H12RSNP.0.PS.A.pwm
PFM	RXRA.H12RSNP.0.PS.A.pfm
Alignment	RXRA.H12RSNP.0.PS.A.words.tsv
Threshold to P-value map	RXRA.H12RSNP.0.PS.A.thr
Motif in other formats
JASPAR format	RXRA.H12RSNP.0.PS.A_jaspar_format.txt
MEME format	RXRA.H12RSNP.0.PS.A_meme_format.meme
Transfac format	RXRA.H12RSNP.0.PS.A_transfac_format.txt
Homer format	RXRA.H12RSNP.0.PS.A_homer_format_0.001.txt RXRA.H12RSNP.0.PS.A_homer_format_0.0005.txt RXRA.H12RSNP.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	173.0	416.0	238.0	173.0
02	436.0	205.0	149.0	210.0
03	347.0	27.0	596.0	30.0
04	706.0	2.0	289.0	3.0
05	10.0	2.0	985.0	3.0
06	2.0	9.0	805.0	184.0
07	3.0	41.0	96.0	860.0
08	3.0	944.0	14.0	39.0
09	988.0	0.0	10.0	2.0

PFM

	A	C	G	T
01	0.173	0.416	0.238	0.173
02	0.436	0.205	0.149	0.21
03	0.347	0.027	0.596	0.03
04	0.706	0.002	0.289	0.003
05	0.01	0.002	0.985	0.003
06	0.002	0.009	0.805	0.184
07	0.003	0.041	0.096	0.86
08	0.003	0.944	0.014	0.039
09	0.988	0.0	0.01	0.002

PWM

	A	C	G	T
01	-0.365	0.506	-0.049	-0.365
02	0.553	-0.197	-0.513	-0.173
03	0.326	-2.171	0.865	-2.071
04	1.034	-4.213	0.144	-3.975
05	-3.066	-4.213	1.366	-3.975
06	-4.213	-3.156	1.165	-0.304
07	-3.975	-1.774	-0.946	1.231
08	-3.975	1.324	-2.773	-1.821
09	1.369	-4.982	-3.066	-4.213

Standard thresholds

P-value	Threshold
0.001	4.764495
0.0005	5.769535
0.0001	7.718975