RXRB.H12INVIVO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRB.H12INVIVO.1.SM.B
Gene (human)	RXRB (GeneCards)
Gene synonyms (human)	NR2B2
Gene (mouse)	Rxrb
Gene synonyms (mouse)	Nr2b2
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	17
Consensus	ndRGGTCAAAGGTCAhv
GC content	49.2%
Information content (bits; total / per base)	20.12 / 1.184
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2384

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)	0.788	0.81	0.659	0.693	0.745	0.761	2.224	2.316	79.796	95.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.99	0.989	0.86	0.862	0.713	0.733
Overall, 3 experiments	best	0.999	0.999	0.916	0.915	0.771	0.784
Methyl HT-SELEX, 1 experiments	median	0.999	0.999	0.916	0.915	0.771	0.784
Methyl HT-SELEX, 1 experiments	best	0.999	0.999	0.916	0.915	0.771	0.784
Non-Methyl HT-SELEX, 2 experiments	median	0.822	0.829	0.715	0.724	0.624	0.641
Non-Methyl HT-SELEX, 2 experiments	best	0.99	0.989	0.86	0.862	0.713	0.733

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.604	0.025	0.4	0.273

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.1.SM.B.pcm
PWM	RXRB.H12INVIVO.1.SM.B.pwm
PFM	RXRB.H12INVIVO.1.SM.B.pfm
Alignment	RXRB.H12INVIVO.1.SM.B.words.tsv
Threshold to P-value map	RXRB.H12INVIVO.1.SM.B.thr
Motif in other formats
JASPAR format	RXRB.H12INVIVO.1.SM.B_jaspar_format.txt
MEME format	RXRB.H12INVIVO.1.SM.B_meme_format.meme
Transfac format	RXRB.H12INVIVO.1.SM.B_transfac_format.txt
Homer format	RXRB.H12INVIVO.1.SM.B_homer_format_0.001.txt RXRB.H12INVIVO.1.SM.B_homer_format_0.0005.txt RXRB.H12INVIVO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	885.5	518.5	489.5	490.5
02	900.75	224.75	1028.75	229.75
03	1262.0	114.0	951.0	57.0
04	73.0	87.0	2154.0	70.0
05	82.0	63.0	2048.0	191.0
06	52.0	128.0	95.0	2109.0
07	98.0	2068.0	90.0	128.0
08	2295.0	32.0	28.0	29.0
09	2233.0	9.0	88.0	54.0
10	2278.0	2.0	103.0	1.0
11	0.0	0.0	2377.0	7.0
12	1.0	2.0	2344.0	37.0
13	7.0	11.0	29.0	2337.0
14	15.0	2215.0	45.0	109.0
15	2183.0	19.0	174.0	8.0
16	753.25	647.25	253.25	730.25
17	546.5	498.5	1002.5	336.5

PFM

	A	C	G	T
01	0.371	0.217	0.205	0.206
02	0.378	0.094	0.432	0.096
03	0.529	0.048	0.399	0.024
04	0.031	0.036	0.904	0.029
05	0.034	0.026	0.859	0.08
06	0.022	0.054	0.04	0.885
07	0.041	0.867	0.038	0.054
08	0.963	0.013	0.012	0.012
09	0.937	0.004	0.037	0.023
10	0.956	0.001	0.043	0.0
11	0.0	0.0	0.997	0.003
12	0.0	0.001	0.983	0.016
13	0.003	0.005	0.012	0.98
14	0.006	0.929	0.019	0.046
15	0.916	0.008	0.073	0.003
16	0.316	0.271	0.106	0.306
17	0.229	0.209	0.421	0.141

PWM

	A	C	G	T
01	0.395	-0.139	-0.196	-0.194
02	0.412	-0.97	0.544	-0.948
03	0.748	-1.64	0.466	-2.317
04	-2.077	-1.905	1.282	-2.118
05	-1.963	-2.22	1.232	-1.131
06	-2.406	-1.526	-1.819	1.261
07	-1.789	1.242	-1.872	-1.526
08	1.346	-2.869	-2.994	-2.961
09	1.318	-4.001	-1.894	-2.369
10	1.338	-5.021	-1.74	-5.314
11	-5.729	-5.729	1.381	-4.202
12	-5.314	-5.021	1.367	-2.731
13	-4.202	-3.833	-2.961	1.364
14	-3.564	1.31	-2.545	-1.684
15	1.296	-3.352	-1.223	-4.097
16	0.233	0.082	-0.851	0.203
17	-0.086	-0.178	0.519	-0.569

Standard thresholds

P-value	Threshold
0.001	-0.23869
0.0005	1.26336
0.0001	4.42986