RXRA.H12INVIVO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRA.H12INVIVO.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	bhRRGGTCA
GC content	52.03%
Information content (bits; total / per base)	9.547 / 1.061
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1014

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)	0.749	0.834	0.584	0.672	0.722	0.808	1.948	2.312	87.288	167.886
Mouse	47 (263)	0.789	0.873	0.644	0.76	0.746	0.869	2.02	2.695	79.886	218.77

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 7 experiments	median	0.883	0.856	0.731	0.73	0.615	0.642
Overall, 7 experiments	best	0.997	0.996	0.96	0.956	0.78	0.807
Methyl HT-SELEX, 1 experiments	median	0.65	0.648	0.58	0.582	0.543	0.549
Methyl HT-SELEX, 1 experiments	best	0.65	0.648	0.58	0.582	0.543	0.549
Non-Methyl HT-SELEX, 6 experiments	median	0.897	0.875	0.735	0.735	0.625	0.643
Non-Methyl HT-SELEX, 6 experiments	best	0.997	0.996	0.96	0.956	0.78	0.807

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	6.456	4.935	0.198	0.112

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.H12INVIVO.0.PS.A.pcm
PWM	RXRA.H12INVIVO.0.PS.A.pwm
PFM	RXRA.H12INVIVO.0.PS.A.pfm
Alignment	RXRA.H12INVIVO.0.PS.A.words.tsv
Threshold to P-value map	RXRA.H12INVIVO.0.PS.A.thr
Motif in other formats
JASPAR format	RXRA.H12INVIVO.0.PS.A_jaspar_format.txt
MEME format	RXRA.H12INVIVO.0.PS.A_meme_format.meme
Transfac format	RXRA.H12INVIVO.0.PS.A_transfac_format.txt
Homer format	RXRA.H12INVIVO.0.PS.A_homer_format_0.001.txt RXRA.H12INVIVO.0.PS.A_homer_format_0.0005.txt RXRA.H12INVIVO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	184.0	437.0	196.0	197.0
02	479.0	165.0	121.0	249.0
03	395.0	77.0	488.0	54.0
04	670.0	4.0	326.0	14.0
05	31.0	1.0	970.0	12.0
06	6.0	4.0	881.0	123.0
07	26.0	21.0	74.0	893.0
08	5.0	951.0	21.0	37.0
09	996.0	6.0	5.0	7.0

PFM

	A	C	G	T
01	0.181	0.431	0.193	0.194
02	0.472	0.163	0.119	0.246
03	0.39	0.076	0.481	0.053
04	0.661	0.004	0.321	0.014
05	0.031	0.001	0.957	0.012
06	0.006	0.004	0.869	0.121
07	0.026	0.021	0.073	0.881
08	0.005	0.938	0.021	0.036
09	0.982	0.006	0.005	0.007

PWM

	A	C	G	T
01	-0.318	0.542	-0.255	-0.25
02	0.633	-0.426	-0.732	-0.018
03	0.441	-1.176	0.652	-1.522
04	0.968	-3.796	0.25	-2.787
05	-2.054	-4.538	1.337	-2.923
06	-3.497	-3.796	1.241	-0.716
07	-2.22	-2.418	-1.215	1.254
08	-3.636	1.317	-2.418	-1.886
09	1.363	-3.497	-3.636	-3.375

Standard thresholds

P-value	Threshold
0.001	4.807675
0.0005	5.697845
0.0001	7.58978