RXRA.H13CORE.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRA.H13CORE.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	bhRAGGTCA
GC content	54.0%
Information content (bits; total / per base)	9.935 / 1.104
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1000
Previous names	RXRA.H12CORE.0.PS.A

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)	0.75	0.826	0.579	0.664	0.73	0.81	1.952	2.335	82.943	184.208
Mouse	47 (263)	0.781	0.878	0.64	0.77	0.743	0.872	2.026	2.698	79.796	219.824

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 7 experiments	median	0.887	0.857	0.735	0.739	0.618	0.643
Overall, 7 experiments	best	0.997	0.993	0.959	0.954	0.782	0.807
Methyl HT-SELEX, 1 experiments	median	0.66	0.649	0.583	0.583	0.543	0.55
Methyl HT-SELEX, 1 experiments	best	0.66	0.649	0.583	0.583	0.543	0.55
Non-Methyl HT-SELEX, 6 experiments	median	0.898	0.873	0.744	0.74	0.629	0.647
Non-Methyl HT-SELEX, 6 experiments	best	0.997	0.993	0.959	0.954	0.782	0.807

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	7.173	5.689	0.201	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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	RXRA.H13CORE.0.PS.A.pcm
PWM	RXRA.H13CORE.0.PS.A.pwm
PFM	RXRA.H13CORE.0.PS.A.pfm
Threshold to P-value map	RXRA.H13CORE.0.PS.A.thr
Motif in other formats
JASPAR format	RXRA.H13CORE.0.PS.A_jaspar_format.txt
MEME format	RXRA.H13CORE.0.PS.A_meme_format.meme
Transfac format	RXRA.H13CORE.0.PS.A_transfac_format.txt
Homer format	RXRA.H13CORE.0.PS.A_homer_format_0.001.txt RXRA.H13CORE.0.PS.A_homer_format_0.0005.txt RXRA.H13CORE.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	163.0	419.0	239.0	179.0
02	441.0	211.0	149.0	199.0
03	355.0	30.0	582.0	33.0
04	693.0	3.0	301.0	3.0
05	7.0	2.0	988.0	3.0
06	2.0	8.0	823.0	167.0
07	3.0	32.0	109.0	856.0
08	2.0	939.0	14.0	45.0
09	987.0	0.0	11.0	2.0

PFM

	A	C	G	T
01	0.163	0.419	0.239	0.179
02	0.441	0.211	0.149	0.199
03	0.355	0.03	0.582	0.033
04	0.693	0.003	0.301	0.003
05	0.007	0.002	0.988	0.003
06	0.002	0.008	0.823	0.167
07	0.003	0.032	0.109	0.856
08	0.002	0.939	0.014	0.045
09	0.987	0.0	0.011	0.002

PWM

	A	C	G	T
01	-0.424	0.514	-0.045	-0.331
02	0.565	-0.168	-0.513	-0.226
03	0.349	-2.071	0.841	-1.981
04	1.015	-3.975	0.184	-3.975
05	-3.362	-4.213	1.369	-3.975
06	-4.213	-3.253	1.187	-0.4
07	-3.975	-2.01	-0.821	1.226
08	-4.213	1.318	-2.773	-1.684
09	1.368	-4.982	-2.985	-4.213

Standard thresholds

P-value	Threshold
0.001	4.816755
0.0005	5.756165
0.0001	7.7038