RXRA.H12RSNP.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRA.H12RSNP.2.SM.B
Gene (human)	RXRA (GeneCards)
Gene synonyms (human)	NR2B1
Gene (mouse)	Rxra
Gene synonyms (mouse)	Nr2b1
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	16
Consensus	nnRGGTCAAAGGTCAh
GC content	46.24%
Information content (bits; total / per base)	21.29 / 1.331
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2396

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)	0.756	0.821	0.633	0.701	0.697	0.771	1.964	2.298	52.62	111.201
Mouse	47 (263)	0.684	0.8	0.539	0.666	0.651	0.772	1.793	2.374	40.721	107.42

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 7 experiments	median	0.818	0.828	0.659	0.677	0.581	0.602
Overall, 7 experiments	best	1.0	1.0	0.945	0.948	0.762	0.794
Methyl HT-SELEX, 1 experiments	median	0.642	0.667	0.562	0.583	0.531	0.547
Methyl HT-SELEX, 1 experiments	best	0.642	0.667	0.562	0.583	0.531	0.547
Non-Methyl HT-SELEX, 6 experiments	median	0.86	0.867	0.684	0.704	0.593	0.619
Non-Methyl HT-SELEX, 6 experiments	best	1.0	1.0	0.945	0.948	0.762	0.794

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.227	4.177	0.141	0.095

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.H12RSNP.2.SM.B.pcm
PWM	RXRA.H12RSNP.2.SM.B.pwm
PFM	RXRA.H12RSNP.2.SM.B.pfm
Alignment	RXRA.H12RSNP.2.SM.B.words.tsv
Threshold to P-value map	RXRA.H12RSNP.2.SM.B.thr
Motif in other formats
JASPAR format	RXRA.H12RSNP.2.SM.B_jaspar_format.txt
MEME format	RXRA.H12RSNP.2.SM.B_meme_format.meme
Transfac format	RXRA.H12RSNP.2.SM.B_transfac_format.txt
Homer format	RXRA.H12RSNP.2.SM.B_homer_format_0.001.txt RXRA.H12RSNP.2.SM.B_homer_format_0.0005.txt RXRA.H12RSNP.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	894.75	432.75	399.75	668.75
02	1025.25	256.25	858.25	256.25
03	1527.0	47.0	796.0	26.0
04	25.0	16.0	2328.0	27.0
05	29.0	15.0	2143.0	209.0
06	16.0	78.0	27.0	2275.0
07	68.0	2225.0	32.0	71.0
08	2364.0	9.0	8.0	15.0
09	2304.0	9.0	46.0	37.0
10	2351.0	5.0	40.0	0.0
11	12.0	5.0	2372.0	7.0
12	6.0	12.0	2308.0	70.0
13	8.0	11.0	22.0	2355.0
14	21.0	2088.0	66.0	221.0
15	2105.5	28.5	244.5	17.5
16	894.25	473.25	326.25	702.25

PFM

	A	C	G	T
01	0.373	0.181	0.167	0.279
02	0.428	0.107	0.358	0.107
03	0.637	0.02	0.332	0.011
04	0.01	0.007	0.972	0.011
05	0.012	0.006	0.894	0.087
06	0.007	0.033	0.011	0.949
07	0.028	0.929	0.013	0.03
08	0.987	0.004	0.003	0.006
09	0.962	0.004	0.019	0.015
10	0.981	0.002	0.017	0.0
11	0.005	0.002	0.99	0.003
12	0.003	0.005	0.963	0.029
13	0.003	0.005	0.009	0.983
14	0.009	0.871	0.028	0.092
15	0.879	0.012	0.102	0.007
16	0.373	0.198	0.136	0.293

PWM

	A	C	G	T
01	0.4	-0.324	-0.403	0.11
02	0.536	-0.845	0.359	-0.845
03	0.934	-2.508	0.284	-3.068
04	-3.105	-3.511	1.355	-3.033
05	-2.966	-3.569	1.272	-1.047
06	-3.511	-2.017	-3.033	1.332
07	-2.151	1.31	-2.874	-2.109
08	1.37	-4.006	-4.101	-3.569
09	1.345	-4.006	-2.528	-2.736
10	1.365	-4.46	-2.662	-5.733
11	-3.763	-4.46	1.374	-4.207
12	-4.326	-3.763	1.346	-2.123
13	-4.101	-3.838	-3.223	1.367
14	-3.265	1.246	-2.18	-0.992
15	1.255	-2.983	-0.891	-3.431
16	0.4	-0.235	-0.605	0.159

Standard thresholds

P-value	Threshold
0.001	-1.39169
0.0005	0.18296
0.0001	3.56861