RXRA.H12INVITRO.1.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRA.H12INVITRO.1.S.C
Gene (human)	RXRA (GeneCards)
Gene synonyms (human)	NR2B1
Gene (mouse)	Rxra
Gene synonyms (mouse)	Nr2b1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	C

Motif length	14
Consensus	nnvRGGTCAWRRSb
GC content	51.58%
Information content (bits; total / per base)	13.347 / 0.953
Data sources	HT-SELEX
Aligned words	2467

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)	0.733	0.801	0.565	0.629	0.696	0.769	1.818	2.149	69.247	105.886
Mouse	47 (263)	0.751	0.861	0.59	0.715	0.708	0.828	1.883	2.476	62.854	198.377

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 7 experiments	median	0.901	0.889	0.735	0.74	0.617	0.646
Overall, 7 experiments	best	0.999	0.999	0.965	0.963	0.784	0.812
Methyl HT-SELEX, 1 experiments	median	0.664	0.673	0.579	0.591	0.546	0.555
Methyl HT-SELEX, 1 experiments	best	0.664	0.673	0.579	0.591	0.546	0.555
Non-Methyl HT-SELEX, 6 experiments	median	0.91	0.9	0.735	0.744	0.621	0.646
Non-Methyl HT-SELEX, 6 experiments	best	0.999	0.999	0.965	0.963	0.784	0.812

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.459	4.525	0.187	0.116

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.H12INVITRO.1.S.C.pcm
PWM	RXRA.H12INVITRO.1.S.C.pwm
PFM	RXRA.H12INVITRO.1.S.C.pfm
Alignment	RXRA.H12INVITRO.1.S.C.words.tsv
Threshold to P-value map	RXRA.H12INVITRO.1.S.C.thr
Motif in other formats
JASPAR format	RXRA.H12INVITRO.1.S.C_jaspar_format.txt
MEME format	RXRA.H12INVITRO.1.S.C_meme_format.meme
Transfac format	RXRA.H12INVITRO.1.S.C_transfac_format.txt
Homer format	RXRA.H12INVITRO.1.S.C_homer_format_0.001.txt RXRA.H12INVITRO.1.S.C_homer_format_0.0005.txt RXRA.H12INVITRO.1.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	542.75	908.75	466.75	548.75
02	923.75	666.75	386.75	489.75
03	864.25	341.25	1031.25	230.25
04	1681.0	27.0	744.0	15.0
05	13.0	13.0	2406.0	35.0
06	5.0	9.0	2377.0	76.0
07	1.0	3.0	25.0	2438.0
08	0.0	2425.0	11.0	31.0
09	2389.0	0.0	77.0	1.0
10	1553.0	225.0	65.0	624.0
11	1805.0	78.0	509.0	75.0
12	453.75	113.75	1765.75	133.75
13	276.75	308.75	1575.75	305.75
14	267.0	503.0	753.0	944.0

PFM

	A	C	G	T
01	0.22	0.368	0.189	0.222
02	0.374	0.27	0.157	0.199
03	0.35	0.138	0.418	0.093
04	0.681	0.011	0.302	0.006
05	0.005	0.005	0.975	0.014
06	0.002	0.004	0.964	0.031
07	0.0	0.001	0.01	0.988
08	0.0	0.983	0.004	0.013
09	0.968	0.0	0.031	0.0
10	0.63	0.091	0.026	0.253
11	0.732	0.032	0.206	0.03
12	0.184	0.046	0.716	0.054
13	0.112	0.125	0.639	0.124
14	0.108	0.204	0.305	0.383

PWM

	A	C	G	T
01	-0.127	0.387	-0.278	-0.116
02	0.403	0.078	-0.465	-0.23
03	0.336	-0.589	0.513	-0.98
04	1.001	-3.062	0.187	-3.597
05	-3.723	-3.723	1.359	-2.818
06	-4.488	-4.034	1.347	-2.072
07	-5.345	-4.828	-3.134	1.372
08	-5.758	1.367	-3.866	-2.933
09	1.352	-5.758	-2.059	-5.345
10	0.922	-1.003	-2.224	0.012
11	1.072	-2.046	-0.191	-2.084
12	-0.306	-1.677	1.05	-1.517
13	-0.797	-0.689	0.936	-0.698
14	-0.833	-0.203	0.199	0.425

Standard thresholds

P-value	Threshold
0.001	3.32326
0.0005	4.53361
0.0001	7.030415