RXRB.H12INVITRO.0.P.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RXRB.H12INVITRO.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	12
Consensus	hhRAGGKCAvdd
GC content	53.19%
Information content (bits; total / per base)	9.52 / 0.793
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)	0.774	0.786	0.607	0.635	0.781	0.788	2.296	2.389	85.06	97.022

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.974	0.965	0.882	0.87	0.728	0.744
Overall, 3 experiments	best	0.984	0.977	0.915	0.904	0.772	0.78
Methyl HT-SELEX, 1 experiments	median	0.984	0.977	0.915	0.904	0.772	0.78
Methyl HT-SELEX, 1 experiments	best	0.984	0.977	0.915	0.904	0.772	0.78
Non-Methyl HT-SELEX, 2 experiments	median	0.817	0.81	0.726	0.726	0.63	0.645
Non-Methyl HT-SELEX, 2 experiments	best	0.974	0.965	0.882	0.87	0.728	0.744

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.536	0.023	0.542	0.242

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.0.P.C.pcm
PWM	RXRB.H12INVITRO.0.P.C.pwm
PFM	RXRB.H12INVITRO.0.P.C.pfm
Alignment	RXRB.H12INVITRO.0.P.C.words.tsv
Threshold to P-value map	RXRB.H12INVITRO.0.P.C.thr
Motif in other formats
JASPAR format	RXRB.H12INVITRO.0.P.C_jaspar_format.txt
MEME format	RXRB.H12INVITRO.0.P.C_meme_format.meme
Transfac format	RXRB.H12INVITRO.0.P.C_transfac_format.txt
Homer format	RXRB.H12INVITRO.0.P.C_homer_format_0.001.txt RXRB.H12INVITRO.0.P.C_homer_format_0.0005.txt RXRB.H12INVITRO.0.P.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	170.0	496.0	163.0	172.0
02	494.0	253.0	74.0	180.0
03	474.0	76.0	414.0	37.0
04	781.0	10.0	196.0	14.0
05	16.0	5.0	968.0	12.0
06	27.0	14.0	806.0	154.0
07	89.0	94.0	99.0	719.0
08	13.0	904.0	58.0	26.0
09	981.0	4.0	7.0	9.0
10	328.0	203.0	371.0	99.0
11	367.0	118.0	353.0	163.0
12	142.0	122.0	581.0	156.0

PFM

	A	C	G	T
01	0.17	0.496	0.163	0.172
02	0.494	0.253	0.074	0.18
03	0.474	0.076	0.414	0.037
04	0.78	0.01	0.196	0.014
05	0.016	0.005	0.967	0.012
06	0.027	0.014	0.805	0.154
07	0.089	0.094	0.099	0.718
08	0.013	0.903	0.058	0.026
09	0.98	0.004	0.007	0.009
10	0.328	0.203	0.371	0.099
11	0.367	0.118	0.353	0.163
12	0.142	0.122	0.58	0.156

PWM

	A	C	G	T
01	-0.383	0.681	-0.425	-0.372
02	0.677	0.011	-1.202	-0.327
03	0.636	-1.176	0.501	-1.873
04	1.133	-3.067	-0.242	-2.774
05	-2.654	-3.623	1.348	-2.91
06	-2.171	-2.774	1.165	-0.481
07	-1.021	-0.968	-0.917	1.051
08	-2.84	1.279	-1.44	-2.207
09	1.361	-3.784	-3.363	-3.157
10	0.269	-0.208	0.392	-0.917
11	0.381	-0.744	0.342	-0.425
12	-0.561	-0.711	0.838	-0.468

Standard thresholds

P-value	Threshold
0.001	4.870365
0.0005	5.693115
0.0001	7.318855