RXRB.H14INVITRO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRB.H14INVITRO.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	16
Consensus	nRRGGTCAAAGGTYRn
GC content	50.6%
Information content (bits; total / per base)	17.054 / 1.066
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	7658
Previous names	RXRB.H12INVITRO.1.SM.B

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)	0.75	0.771	0.595	0.622	0.711	0.73	1.964	2.049	66.319	82.26

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.991	0.99	0.871	0.87	0.725	0.743
Overall, 3 experiments	best	0.999	0.999	0.916	0.914	0.772	0.784
Methyl HT-SELEX, 1 experiments	median	0.999	0.999	0.916	0.914	0.772	0.784
Methyl HT-SELEX, 1 experiments	best	0.999	0.999	0.916	0.914	0.772	0.784
Non-Methyl HT-SELEX, 2 experiments	median	0.835	0.838	0.727	0.734	0.633	0.649
Non-Methyl HT-SELEX, 2 experiments	best	0.991	0.99	0.871	0.87	0.725	0.743

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.602	0.016	0.453	0.152

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	RXRB.H14INVITRO.1.SM.B.pcm
PWM	RXRB.H14INVITRO.1.SM.B.pwm
PFM	RXRB.H14INVITRO.1.SM.B.pfm
Threshold to P-value map	RXRB.H14INVITRO.1.SM.B.thr
Motif in other formats
JASPAR format	RXRB.H14INVITRO.1.SM.B_jaspar_format.txt
MEME format	RXRB.H14INVITRO.1.SM.B_meme_format.meme
Transfac format	RXRB.H14INVITRO.1.SM.B_transfac_format.txt
Homer format	RXRB.H14INVITRO.1.SM.B_homer_format_0.001.txt RXRB.H14INVITRO.1.SM.B_homer_format_0.0005.txt RXRB.H14INVITRO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2721.25	1691.25	1537.25	1708.25
02	2447.25	567.25	4102.25	541.25
03	3860.0	92.0	3671.0	35.0
04	85.0	40.0	7444.0	89.0
05	27.0	13.0	7011.0	607.0
06	16.0	38.0	182.0	7422.0
07	43.0	6794.0	336.0	485.0
08	7580.0	4.0	63.0	11.0
09	6484.0	281.0	378.0	515.0
10	6112.0	205.0	1214.0	127.0
11	336.0	244.0	6850.0	228.0
12	239.0	248.0	6515.0	656.0
13	244.0	286.0	944.0	6184.0
14	304.0	5478.0	746.0	1130.0
15	5571.0	609.0	1119.0	359.0
16	2372.5	2006.5	1289.5	1989.5

PFM

	A	C	G	T
01	0.355	0.221	0.201	0.223
02	0.32	0.074	0.536	0.071
03	0.504	0.012	0.479	0.005
04	0.011	0.005	0.972	0.012
05	0.004	0.002	0.916	0.079
06	0.002	0.005	0.024	0.969
07	0.006	0.887	0.044	0.063
08	0.99	0.001	0.008	0.001
09	0.847	0.037	0.049	0.067
10	0.798	0.027	0.159	0.017
11	0.044	0.032	0.894	0.03
12	0.031	0.032	0.851	0.086
13	0.032	0.037	0.123	0.808
14	0.04	0.715	0.097	0.148
15	0.727	0.08	0.146	0.047
16	0.31	0.262	0.168	0.26

PWM

	A	C	G	T
01	0.351	-0.124	-0.219	-0.114
02	0.245	-1.214	0.761	-1.26
03	0.701	-3.013	0.65	-3.941
04	-3.09	-3.815	1.357	-3.045
05	-4.183	-4.835	1.297	-1.146
06	-4.655	-3.864	-2.342	1.354
07	-3.746	1.266	-1.735	-1.37
08	1.375	-5.728	-3.38	-4.975
09	1.219	-1.912	-1.618	-1.31
10	1.16	-2.225	-0.455	-2.697
11	-1.735	-2.052	1.274	-2.119
12	-2.073	-2.036	1.224	-1.069
13	-2.052	-1.895	-0.706	1.172
14	-1.834	1.051	-0.941	-0.526
15	1.067	-1.143	-0.536	-1.669
16	0.214	0.047	-0.395	0.038

Standard thresholds

P-value	Threshold
0.001	1.87601
0.0005	3.16941
0.0001	5.87671