NR2C1.H12INVITRO.1.PM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR2C1.H12INVITRO.1.PM.A
Gene (human)	NR2C1 (GeneCards)
Gene synonyms (human)	TR2
Gene (mouse)	Nr2c1
Gene synonyms (mouse)	Tr2, Tr2-11
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	16
Consensus	ndAGGTCAWRRSbbdn
GC content	53.31%
Information content (bits; total / per base)	13.555 / 0.847
Data sources	ChIP-Seq + Methyl-HT-SELEX
Aligned words	2394

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	3 (21)	0.717	0.817	0.629	0.752	0.702	0.82	2.669	3.663	70.585	164.699

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.976	0.963	0.957	0.937	0.922	0.897
Overall, 2 experiments	best	0.991	0.987	0.98	0.971	0.958	0.942
Methyl HT-SELEX, 1 experiments	median	0.991	0.987	0.98	0.971	0.958	0.942
Methyl HT-SELEX, 1 experiments	best	0.991	0.987	0.98	0.971	0.958	0.942
Non-Methyl HT-SELEX, 1 experiments	median	0.961	0.939	0.934	0.903	0.886	0.852
Non-Methyl HT-SELEX, 1 experiments	best	0.961	0.939	0.934	0.903	0.886	0.852

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.02	5.349	0.235	0.097

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.594	0.051	0.595	0.463

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	TR (NR2C) {2.1.3.4} (TFClass)
TFClass ID	TFClass: 2.1.3.4.1
HGNC	HGNC:7971
MGI	MGI:1352465
EntrezGene (human)	GeneID:7181 (SSTAR profile)
EntrezGene (mouse)	GeneID:22025 (SSTAR profile)
UniProt ID (human)	NR2C1_HUMAN
UniProt ID (mouse)	NR2C1_MOUSE
UniProt AC (human)	P13056 (TFClass)
UniProt AC (mouse)	Q505F1 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 0 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	NR2C1.H12INVITRO.1.PM.A.pcm
PWM	NR2C1.H12INVITRO.1.PM.A.pwm
PFM	NR2C1.H12INVITRO.1.PM.A.pfm
Alignment	NR2C1.H12INVITRO.1.PM.A.words.tsv
Threshold to P-value map	NR2C1.H12INVITRO.1.PM.A.thr
Motif in other formats
JASPAR format	NR2C1.H12INVITRO.1.PM.A_jaspar_format.txt
MEME format	NR2C1.H12INVITRO.1.PM.A_meme_format.meme
Transfac format	NR2C1.H12INVITRO.1.PM.A_transfac_format.txt
Homer format	NR2C1.H12INVITRO.1.PM.A_homer_format_0.001.txt NR2C1.H12INVITRO.1.PM.A_homer_format_0.0005.txt NR2C1.H12INVITRO.1.PM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	685.25	450.25	575.25	683.25
02	988.25	128.25	1011.25	266.25
03	1630.0	10.0	750.0	4.0
04	2.0	3.0	2371.0	18.0
05	0.0	0.0	2367.0	27.0
06	0.0	4.0	53.0	2337.0
07	0.0	2215.0	36.0	143.0
08	2113.0	0.0	280.0	1.0
09	1357.0	285.0	130.0	622.0
10	1335.0	96.0	825.0	138.0
11	359.0	137.0	1820.0	78.0
12	202.0	286.0	1752.0	154.0
13	173.0	305.0	667.0	1249.0
14	153.0	1114.0	539.0	588.0
15	978.5	308.5	780.5	326.5
16	611.25	511.25	609.25	662.25

PFM

	A	C	G	T
01	0.286	0.188	0.24	0.285
02	0.413	0.054	0.422	0.111
03	0.681	0.004	0.313	0.002
04	0.001	0.001	0.99	0.008
05	0.0	0.0	0.989	0.011
06	0.0	0.002	0.022	0.976
07	0.0	0.925	0.015	0.06
08	0.883	0.0	0.117	0.0
09	0.567	0.119	0.054	0.26
10	0.558	0.04	0.345	0.058
11	0.15	0.057	0.76	0.033
12	0.084	0.119	0.732	0.064
13	0.072	0.127	0.279	0.522
14	0.064	0.465	0.225	0.246
15	0.409	0.129	0.326	0.136
16	0.255	0.214	0.254	0.277

PWM

	A	C	G	T
01	0.135	-0.284	-0.039	0.132
02	0.5	-1.529	0.523	-0.806
03	1.0	-3.917	0.225	-4.615
04	-5.025	-4.799	1.374	-3.405
05	-5.732	-5.732	1.373	-3.032
06	-5.732	-4.615	-2.391	1.36
07	-5.732	1.306	-2.762	-1.421
08	1.259	-5.732	-0.756	-5.318
09	0.817	-0.738	-1.515	0.038
10	0.8	-1.813	0.32	-1.456
11	-0.509	-1.464	1.11	-2.016
12	-1.08	-0.735	1.072	-1.348
13	-1.233	-0.671	0.108	0.734
14	-1.355	0.62	-0.104	-0.018
15	0.49	-0.66	0.265	-0.603
16	0.021	-0.157	0.018	0.101

Standard thresholds

P-value	Threshold
0.001	3.28081
0.0005	4.53196
0.0001	7.01686