RXRB.H12INVITRO.2.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRB.H12INVITRO.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	nvRGGTCAddd
GC content	53.76%
Information content (bits; total / per base)	8.887 / 0.808
Data sources	ChIP-Seq + HT-SELEX
Aligned words	5854

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)	0.754	0.767	0.601	0.615	0.737	0.759	2.014	2.117	80.456	102.77

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.981	0.974	0.901	0.89	0.753	0.765
Overall, 3 experiments	best	0.99	0.986	0.941	0.93	0.81	0.813
Methyl HT-SELEX, 1 experiments	median	0.99	0.986	0.941	0.93	0.81	0.813
Methyl HT-SELEX, 1 experiments	best	0.99	0.986	0.941	0.93	0.81	0.813
Non-Methyl HT-SELEX, 2 experiments	median	0.827	0.824	0.745	0.742	0.651	0.661
Non-Methyl HT-SELEX, 2 experiments	best	0.981	0.974	0.901	0.89	0.753	0.765

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.686	0.104	0.358	-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.H12INVITRO.2.PS.A.pcm
PWM	RXRB.H12INVITRO.2.PS.A.pwm
PFM	RXRB.H12INVITRO.2.PS.A.pfm
Alignment	RXRB.H12INVITRO.2.PS.A.words.tsv
Threshold to P-value map	RXRB.H12INVITRO.2.PS.A.thr
Motif in other formats
JASPAR format	RXRB.H12INVITRO.2.PS.A_jaspar_format.txt
MEME format	RXRB.H12INVITRO.2.PS.A_meme_format.meme
Transfac format	RXRB.H12INVITRO.2.PS.A_transfac_format.txt
Homer format	RXRB.H12INVITRO.2.PS.A_homer_format_0.001.txt RXRB.H12INVITRO.2.PS.A_homer_format_0.0005.txt RXRB.H12INVITRO.2.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2115.75	1245.75	1325.75	1166.75
02	1999.0	570.0	2753.0	532.0
03	2837.0	256.0	2292.0	469.0
04	6.0	4.0	5839.0	5.0
05	0.0	0.0	5255.0	599.0
06	0.0	2.0	63.0	5789.0
07	15.0	5090.0	617.0	132.0
08	4198.0	81.0	1517.0	58.0
09	1962.0	900.0	1034.0	1958.0
10	1901.0	652.0	1853.0	1448.0
11	1033.25	821.25	2446.25	1553.25

PFM

	A	C	G	T
01	0.361	0.213	0.226	0.199
02	0.341	0.097	0.47	0.091
03	0.485	0.044	0.392	0.08
04	0.001	0.001	0.997	0.001
05	0.0	0.0	0.898	0.102
06	0.0	0.0	0.011	0.989
07	0.003	0.869	0.105	0.023
08	0.717	0.014	0.259	0.01
09	0.335	0.154	0.177	0.334
10	0.325	0.111	0.317	0.247
11	0.177	0.14	0.418	0.265

PWM

	A	C	G	T
01	0.368	-0.161	-0.099	-0.226
02	0.311	-0.941	0.631	-1.009
03	0.661	-1.736	0.448	-1.135
04	-5.19	-5.471	1.383	-5.32
05	-6.516	-6.516	1.277	-0.891
06	-6.516	-5.862	-3.113	1.374
07	-4.447	1.245	-0.862	-2.391
08	1.053	-2.869	0.036	-3.193
09	0.293	-0.485	-0.347	0.291
10	0.261	-0.807	0.236	-0.011
11	-0.348	-0.577	0.513	0.059

Standard thresholds

P-value	Threshold
0.001	5.263685
0.0005	6.0542
0.0001	7.392285