RXRB.H12RSNP.2.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRB.H12RSNP.2.PS.A
Gene (human)	RXRB (GeneCards)
Gene synonyms (human)	NR2B2
Gene (mouse)	Rxrb
Gene synonyms (mouse)	Nr2b2
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	A

Motif length	11
Consensus	nvdGGTCRndd
GC content	54.26%
Information content (bits; total / per base)	7.509 / 0.683
Data sources	ChIP-Seq + HT-SELEX
Aligned words	7878

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)	0.749	0.763	0.597	0.611	0.735	0.757	2.024	2.132	74.432	94.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.98	0.972	0.899	0.887	0.755	0.764
Overall, 3 experiments	best	0.99	0.986	0.938	0.927	0.812	0.812
Methyl HT-SELEX, 1 experiments	median	0.99	0.986	0.938	0.927	0.812	0.812
Methyl HT-SELEX, 1 experiments	best	0.99	0.986	0.938	0.927	0.812	0.812
Non-Methyl HT-SELEX, 2 experiments	median	0.828	0.822	0.745	0.741	0.654	0.661
Non-Methyl HT-SELEX, 2 experiments	best	0.98	0.972	0.899	0.887	0.755	0.764

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.708	0.106	0.344	-0.03

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.H12RSNP.2.PS.A.pcm
PWM	RXRB.H12RSNP.2.PS.A.pwm
PFM	RXRB.H12RSNP.2.PS.A.pfm
Alignment	RXRB.H12RSNP.2.PS.A.words.tsv
Threshold to P-value map	RXRB.H12RSNP.2.PS.A.thr
Motif in other formats
JASPAR format	RXRB.H12RSNP.2.PS.A_jaspar_format.txt
MEME format	RXRB.H12RSNP.2.PS.A_meme_format.meme
Transfac format	RXRB.H12RSNP.2.PS.A_transfac_format.txt
Homer format	RXRB.H12RSNP.2.PS.A_homer_format_0.001.txt RXRB.H12RSNP.2.PS.A_homer_format_0.0005.txt RXRB.H12RSNP.2.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2777.0	1611.0	1896.0	1594.0
02	2583.25	882.25	3547.25	865.25
03	3637.0	527.0	2866.0	848.0
04	42.0	83.0	7660.0	93.0
05	1.0	0.0	6573.0	1304.0
06	30.0	10.0	356.0	7482.0
07	122.0	6177.0	1272.0	307.0
08	4883.0	198.0	2640.0	157.0
09	2368.0	1266.0	1692.0	2552.0
10	2414.5	940.5	2498.5	2024.5
11	1461.25	1170.25	3158.25	2088.25

PFM

	A	C	G	T
01	0.353	0.204	0.241	0.202
02	0.328	0.112	0.45	0.11
03	0.462	0.067	0.364	0.108
04	0.005	0.011	0.972	0.012
05	0.0	0.0	0.834	0.166
06	0.004	0.001	0.045	0.95
07	0.015	0.784	0.161	0.039
08	0.62	0.025	0.335	0.02
09	0.301	0.161	0.215	0.324
10	0.306	0.119	0.317	0.257
11	0.185	0.149	0.401	0.265

PWM

	A	C	G	T
01	0.343	-0.201	-0.038	-0.211
02	0.271	-0.802	0.588	-0.821
03	0.613	-1.315	0.375	-0.841
04	-3.797	-3.141	1.357	-3.03
05	-6.41	-6.779	1.204	-0.412
06	-4.113	-5.082	-1.705	1.334
07	-2.764	1.142	-0.437	-1.853
08	0.907	-2.287	0.293	-2.516
09	0.184	-0.441	-0.152	0.259
10	0.204	-0.738	0.238	0.028
11	-0.298	-0.52	0.472	0.058

Standard thresholds

P-value	Threshold
0.001	5.326375
0.0005	5.93599
0.0001	7.00196