NR4A1.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR4A1.H12INVIVO.0.PSM.A
Gene (human)	NR4A1 (GeneCards)
Gene synonyms (human)	GFRP1, HMR, NAK1
Gene (mouse)	Nr4a1
Gene synonyms (mouse)	Gfrp, Hmr, N10, Nur77
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	8
Consensus	AAAGGTCA
GC content	38.79%
Information content (bits; total / per base)	12.902 / 1.613
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	999

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	2 (14)	0.885	0.917	0.832	0.871	0.87	0.895	2.886	3.021	211.711	236.26
Mouse	1 (5)	0.903	0.928	0.832	0.864	0.889	0.913	2.963	3.115	319.108	331.131

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.998	0.998	0.995	0.994	0.973	0.968
Overall, 4 experiments	best	1.0	1.0	0.999	0.999	0.998	0.997
Methyl HT-SELEX, 2 experiments	median	0.998	0.998	0.995	0.994	0.973	0.968
Methyl HT-SELEX, 2 experiments	best	0.998	0.998	0.996	0.995	0.984	0.979
Non-Methyl HT-SELEX, 2 experiments	median	0.998	0.997	0.991	0.988	0.965	0.959
Non-Methyl HT-SELEX, 2 experiments	best	1.0	1.0	0.999	0.999	0.998	0.997

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.591	0.095	0.504	0.316

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	Nuclear receptors with C4 zinc fingers {2.1} (TFClass)
TF family	NGFI (NR4A) {2.1.4} (TFClass)
TF subfamily	{2.1.4.0} (TFClass)
TFClass ID	TFClass: 2.1.4.0.1
HGNC	HGNC:7980
MGI	MGI:1352454
EntrezGene (human)	GeneID:3164 (SSTAR profile)
EntrezGene (mouse)	GeneID:15370 (SSTAR profile)
UniProt ID (human)	NR4A1_HUMAN
UniProt ID (mouse)	NR4A1_MOUSE
UniProt AC (human)	P22736 (TFClass)
UniProt AC (mouse)	P12813 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 1 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	NR4A1.H12INVIVO.0.PSM.A.pcm
PWM	NR4A1.H12INVIVO.0.PSM.A.pwm
PFM	NR4A1.H12INVIVO.0.PSM.A.pfm
Alignment	NR4A1.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	NR4A1.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	NR4A1.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	NR4A1.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	NR4A1.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	NR4A1.H12INVIVO.0.PSM.A_homer_format_0.001.txt NR4A1.H12INVIVO.0.PSM.A_homer_format_0.0005.txt NR4A1.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	868.0	0.0	97.0	34.0
02	963.0	6.0	17.0	13.0
03	999.0	0.0	0.0	0.0
04	3.0	0.0	848.0	148.0
05	4.0	2.0	979.0	14.0
06	8.0	84.0	84.0	823.0
07	0.0	961.0	7.0	31.0
08	974.0	9.0	6.0	10.0

PFM

	A	C	G	T
01	0.869	0.0	0.097	0.034
02	0.964	0.006	0.017	0.013
03	1.0	0.0	0.0	0.0
04	0.003	0.0	0.849	0.148
05	0.004	0.002	0.98	0.014
06	0.008	0.084	0.084	0.824
07	0.0	0.962	0.007	0.031
08	0.975	0.009	0.006	0.01

PWM

	A	C	G	T
01	1.241	-4.981	-0.935	-1.951
02	1.344	-3.483	-2.597	-2.838
03	1.381	-4.981	-4.981	-4.981
04	-3.974	-4.981	1.218	-0.519
05	-3.782	-4.212	1.361	-2.772
06	-3.252	-1.076	-1.076	1.188
07	-4.981	1.342	-3.361	-2.039
08	1.356	-3.155	-3.483	-3.065

Standard thresholds

P-value	Threshold
0.001	3.557395
0.0005	4.54981
0.0001	6.82063