NR4A1.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR4A1.H12INVITRO.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	37.59%
Information content (bits; total / per base)	13.108 / 1.639
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	998

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)	0.882	0.915	0.83	0.87	0.867	0.894	2.88	3.018	216.266	254.796
Mouse	1 (5)	0.902	0.925	0.832	0.862	0.89	0.911	2.955	3.097	318.678	333.481

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.998	0.998	0.995	0.994	0.974	0.969
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	0.974	0.969
Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.996	0.995	0.984	0.98
Non-Methyl HT-SELEX, 2 experiments	median	0.998	0.997	0.991	0.988	0.966	0.96
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	0.614	0.081	0.53	0.324

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.H12INVITRO.0.PSM.A.pcm
PWM	NR4A1.H12INVITRO.0.PSM.A.pwm
PFM	NR4A1.H12INVITRO.0.PSM.A.pfm
Alignment	NR4A1.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	NR4A1.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	NR4A1.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	NR4A1.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	NR4A1.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	NR4A1.H12INVITRO.0.PSM.A_homer_format_0.001.txt NR4A1.H12INVITRO.0.PSM.A_homer_format_0.0005.txt NR4A1.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	904.0	2.0	64.0	28.0
02	968.0	1.0	17.0	12.0
03	992.0	1.0	4.0	1.0
04	2.0	2.0	806.0	188.0
05	1.0	1.0	984.0	12.0
06	7.0	60.0	72.0	859.0
07	1.0	963.0	0.0	34.0
08	970.0	18.0	6.0	4.0

PFM

	A	C	G	T
01	0.906	0.002	0.064	0.028
02	0.97	0.001	0.017	0.012
03	0.994	0.001	0.004	0.001
04	0.002	0.002	0.808	0.188
05	0.001	0.001	0.986	0.012
06	0.007	0.06	0.072	0.861
07	0.001	0.965	0.0	0.034
08	0.972	0.018	0.006	0.004

PWM

	A	C	G	T
01	1.282	-4.211	-1.341	-2.134
02	1.351	-4.523	-2.596	-2.907
03	1.375	-4.523	-3.781	-4.523
04	-4.211	-4.211	1.168	-0.281
05	-4.523	-4.523	1.367	-2.907
06	-3.36	-1.404	-1.226	1.231
07	-4.523	1.345	-4.98	-1.95
08	1.353	-2.544	-3.482	-3.781

Standard thresholds

P-value	Threshold
0.001	3.17379
0.0005	4.59167
0.0001	6.84626