RXRG.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRG.H12INVIVO.0.P.B
Gene (human)	RXRG (GeneCards)
Gene synonyms (human)	NR2B3
Gene (mouse)	Rxrg
Gene synonyms (mouse)	Nr2b3
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	10
Consensus	RRGGTCAdRR
GC content	54.56%
Information content (bits; total / per base)	10.723 / 1.072
Data sources	ChIP-Seq
Aligned words	103

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
Mouse	3 (14)	0.713	0.948	0.618	0.875	0.672	0.953	2.338	4.276	32.456	200.444

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.985	0.973	0.977	0.962	0.882	0.881
Overall, 5 experiments	best	0.989	0.981	0.979	0.968	0.965	0.946
Methyl HT-SELEX, 1 experiments	median	0.983	0.971	0.978	0.963	0.965	0.946
Methyl HT-SELEX, 1 experiments	best	0.983	0.971	0.978	0.963	0.965	0.946
Non-Methyl HT-SELEX, 4 experiments	median	0.986	0.976	0.972	0.959	0.855	0.859
Non-Methyl HT-SELEX, 4 experiments	best	0.989	0.981	0.979	0.968	0.948	0.93

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.667	0.324	0.752	0.529

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: 2.1.3.1.3
HGNC	HGNC:10479
MGI	MGI:98216
EntrezGene (human)	GeneID:6258 (SSTAR profile)
EntrezGene (mouse)	GeneID:20183 (SSTAR profile)
UniProt ID (human)	RXRG_HUMAN
UniProt ID (mouse)	RXRG_MOUSE
UniProt AC (human)	P48443 (TFClass)
UniProt AC (mouse)	P28705 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 3 mouse
HT-SELEX	4
Methyl-HT-SELEX	1

PCM	RXRG.H12INVIVO.0.P.B.pcm
PWM	RXRG.H12INVIVO.0.P.B.pwm
PFM	RXRG.H12INVIVO.0.P.B.pfm
Alignment	RXRG.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	RXRG.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	RXRG.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	RXRG.H12INVIVO.0.P.B_meme_format.meme
Transfac format	RXRG.H12INVIVO.0.P.B_transfac_format.txt
Homer format	RXRG.H12INVIVO.0.P.B_homer_format_0.001.txt RXRG.H12INVIVO.0.P.B_homer_format_0.0005.txt RXRG.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	47.0	8.0	43.0	5.0
02	70.0	2.0	24.0	7.0
03	1.0	1.0	100.0	1.0
04	1.0	1.0	72.0	29.0
05	1.0	2.0	8.0	92.0
06	0.0	101.0	2.0	0.0
07	100.0	2.0	0.0	1.0
08	48.0	4.0	37.0	14.0
09	13.0	10.0	72.0	8.0
10	19.0	3.0	70.0	11.0

PFM

	A	C	G	T
01	0.456	0.078	0.417	0.049
02	0.68	0.019	0.233	0.068
03	0.01	0.01	0.971	0.01
04	0.01	0.01	0.699	0.282
05	0.01	0.019	0.078	0.893
06	0.0	0.981	0.019	0.0
07	0.971	0.019	0.0	0.01
08	0.466	0.039	0.359	0.136
09	0.126	0.097	0.699	0.078
10	0.184	0.029	0.68	0.107

PWM

	A	C	G	T
01	0.582	-1.078	0.495	-1.475
02	0.972	-2.142	-0.067	-1.193
03	-2.523	-2.523	1.324	-2.523
04	-2.523	-2.523	1.0	0.114
05	-2.523	-2.142	-1.078	1.242
06	-3.145	1.334	-2.142	-3.145
07	1.324	-2.142	-3.145	-2.523
08	0.603	-1.652	0.349	-0.574
09	-0.642	-0.88	1.0	-1.078
10	-0.289	-1.867	0.972	-0.794

Standard thresholds

P-value	Threshold
0.001	4.755535
0.0005	5.601835
0.0001	7.280155