RXRB.H12INVIVO.0.P.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRB.H12INVIVO.0.P.C
Gene (human)	RXRB (GeneCards)
Gene synonyms (human)	NR2B2
Gene (mouse)	Rxrb
Gene synonyms (mouse)	Nr2b2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	C

Motif length	14
Consensus	dRdnbMRAGKYCAv
GC content	53.04%
Information content (bits; total / per base)	9.72 / 0.694
Data sources	ChIP-Seq
Aligned words	1001

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	1 (7)	0.791	0.811	0.676	0.702	0.775	0.791	2.496	2.579	85.602	104.409

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.977	0.973	0.85	0.847	0.705	0.724
Overall, 3 experiments	best	0.989	0.986	0.895	0.888	0.753	0.764
Methyl HT-SELEX, 1 experiments	median	0.989	0.986	0.895	0.888	0.753	0.764
Methyl HT-SELEX, 1 experiments	best	0.989	0.986	0.895	0.888	0.753	0.764
Non-Methyl HT-SELEX, 2 experiments	median	0.803	0.804	0.703	0.708	0.616	0.631
Non-Methyl HT-SELEX, 2 experiments	best	0.977	0.973	0.85	0.847	0.705	0.724

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.582	0.019	0.541	0.303

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: 2.1.3.1.2
HGNC	HGNC:10478
MGI	MGI:98215
EntrezGene (human)	GeneID:6257 (SSTAR profile)
EntrezGene (mouse)	GeneID:20182 (SSTAR profile)
UniProt ID (human)	RXRB_HUMAN
UniProt ID (mouse)	RXRB_MOUSE
UniProt AC (human)	P28702 (TFClass)
UniProt AC (mouse)	P28704 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	2
Methyl-HT-SELEX	1

PCM	RXRB.H12INVIVO.0.P.C.pcm
PWM	RXRB.H12INVIVO.0.P.C.pwm
PFM	RXRB.H12INVIVO.0.P.C.pfm
Alignment	RXRB.H12INVIVO.0.P.C.words.tsv
Threshold to P-value map	RXRB.H12INVIVO.0.P.C.thr
Motif in other formats
JASPAR format	RXRB.H12INVIVO.0.P.C_jaspar_format.txt
MEME format	RXRB.H12INVIVO.0.P.C_meme_format.meme
Transfac format	RXRB.H12INVIVO.0.P.C_transfac_format.txt
Homer format	RXRB.H12INVIVO.0.P.C_homer_format_0.001.txt RXRB.H12INVIVO.0.P.C_homer_format_0.0005.txt RXRB.H12INVIVO.0.P.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	435.0	49.0	337.0	180.0
02	188.0	97.0	615.0	101.0
03	261.0	92.0	539.0	109.0
04	188.0	190.0	368.0	255.0
05	102.0	554.0	142.0	203.0
06	637.0	249.0	37.0	78.0
07	633.0	42.0	311.0	15.0
08	799.0	13.0	161.0	28.0
09	13.0	3.0	959.0	26.0
10	46.0	23.0	730.0	202.0
11	101.0	160.0	129.0	611.0
12	32.0	834.0	74.0	61.0
13	927.0	12.0	37.0	25.0
14	208.0	247.0	429.0	117.0

PFM

	A	C	G	T
01	0.435	0.049	0.337	0.18
02	0.188	0.097	0.614	0.101
03	0.261	0.092	0.538	0.109
04	0.188	0.19	0.368	0.255
05	0.102	0.553	0.142	0.203
06	0.636	0.249	0.037	0.078
07	0.632	0.042	0.311	0.015
08	0.798	0.013	0.161	0.028
09	0.013	0.003	0.958	0.026
10	0.046	0.023	0.729	0.202
11	0.101	0.16	0.129	0.61
12	0.032	0.833	0.074	0.061
13	0.926	0.012	0.037	0.025
14	0.208	0.247	0.429	0.117

PWM

	A	C	G	T
01	0.55	-1.603	0.296	-0.327
02	-0.284	-0.937	0.895	-0.897
03	0.042	-0.989	0.764	-0.822
04	-0.284	-0.273	0.383	0.019
05	-0.888	0.791	-0.561	-0.208
06	0.93	-0.005	-1.873	-1.151
07	0.924	-1.751	0.216	-2.712
08	1.156	-2.84	-0.437	-2.137
09	-2.84	-3.976	1.338	-2.207
10	-1.664	-2.321	1.066	-0.213
11	-0.897	-0.443	-0.656	0.889
12	-2.011	1.199	-1.202	-1.391
13	1.304	-2.91	-1.873	-2.244
14	-0.184	-0.013	0.536	-0.753

Standard thresholds

P-value	Threshold
0.001	4.76681
0.0005	5.56591
0.0001	7.20361