RXRA.H12INVITRO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRA.H12INVITRO.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	10
Consensus	nvRGGTCRhd
GC content	51.76%
Information content (bits; total / per base)	8.767 / 0.877
Data sources	ChIP-Seq + HT-SELEX
Aligned words	9729

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)	0.738	0.811	0.581	0.654	0.697	0.776	1.78	2.05	83.32	144.237
Mouse	47 (263)	0.773	0.894	0.619	0.773	0.716	0.859	1.818	2.441	76.745	234.602

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 7 experiments	median	0.921	0.898	0.733	0.746	0.616	0.645
Overall, 7 experiments	best	0.996	0.994	0.965	0.961	0.781	0.81
Methyl HT-SELEX, 1 experiments	median	0.652	0.657	0.566	0.58	0.533	0.546
Methyl HT-SELEX, 1 experiments	best	0.652	0.657	0.566	0.58	0.533	0.546
Non-Methyl HT-SELEX, 6 experiments	median	0.922	0.903	0.756	0.757	0.636	0.658
Non-Methyl HT-SELEX, 6 experiments	best	0.996	0.994	0.965	0.961	0.781	0.81

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.133	2.578	0.188	0.109

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.0.PS.A.pcm
PWM	RXRA.H12INVITRO.0.PS.A.pwm
PFM	RXRA.H12INVITRO.0.PS.A.pfm
Alignment	RXRA.H12INVITRO.0.PS.A.words.tsv
Threshold to P-value map	RXRA.H12INVITRO.0.PS.A.thr
Motif in other formats
JASPAR format	RXRA.H12INVITRO.0.PS.A_jaspar_format.txt
MEME format	RXRA.H12INVITRO.0.PS.A_meme_format.meme
Transfac format	RXRA.H12INVITRO.0.PS.A_transfac_format.txt
Homer format	RXRA.H12INVITRO.0.PS.A_homer_format_0.001.txt RXRA.H12INVITRO.0.PS.A_homer_format_0.0005.txt RXRA.H12INVITRO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3874.25	2167.25	1704.25	1983.25
02	3217.0	1054.0	4428.0	1030.0
03	5160.5	321.5	4008.5	238.5
04	39.0	14.0	9227.0	449.0
05	10.0	39.0	8773.0	907.0
06	0.0	4.0	103.0	9622.0
07	46.0	8777.0	233.0	673.0
08	7220.75	288.75	1973.75	245.75
09	3518.75	1838.75	1235.75	3135.75
10	4187.5	1361.5	2800.5	1379.5

PFM

	A	C	G	T
01	0.398	0.223	0.175	0.204
02	0.331	0.108	0.455	0.106
03	0.53	0.033	0.412	0.025
04	0.004	0.001	0.948	0.046
05	0.001	0.004	0.902	0.093
06	0.0	0.0	0.011	0.989
07	0.005	0.902	0.024	0.069
08	0.742	0.03	0.203	0.025
09	0.362	0.189	0.127	0.322
10	0.43	0.14	0.288	0.142

PWM

	A	C	G	T
01	0.465	-0.115	-0.355	-0.204
02	0.279	-0.835	0.599	-0.858
03	0.752	-2.017	0.499	-2.314
04	-4.077	-5.007	1.333	-1.685
05	-5.288	-4.077	1.282	-0.985
06	-6.966	-5.958	-3.141	1.375
07	-3.92	1.283	-2.337	-1.282
08	1.088	-2.124	-0.209	-2.284
09	0.369	-0.279	-0.676	0.254
10	0.543	-0.579	0.141	-0.566

Standard thresholds

P-value	Threshold
0.001	5.100715
0.0005	5.925845
0.0001	7.404745