EGR3.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	EGR3.H12RSNP.0.PSM.A
Gene (human)	EGR3 (GeneCards)
Gene synonyms (human)	PILOT
Gene (mouse)	Egr3
Gene synonyms (mouse)	Egr-3
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	bRCGTGGGCGKdn
GC content	70.42%
Information content (bits; total / per base)	13.392 / 1.03
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	5943

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 (5)	0.851	0.901	0.7	0.783	0.841	0.847	2.671	2.695	110.252	171.046

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.644	0.665	0.566	0.583	0.537	0.548
Overall, 6 experiments	best	0.999	0.998	0.999	0.998	0.997	0.996
Methyl HT-SELEX, 1 experiments	median	0.99	0.987	0.815	0.835	0.642	0.693
Methyl HT-SELEX, 1 experiments	best	0.99	0.987	0.815	0.835	0.642	0.693
Non-Methyl HT-SELEX, 5 experiments	median	0.616	0.634	0.555	0.567	0.533	0.539
Non-Methyl HT-SELEX, 5 experiments	best	0.999	0.998	0.999	0.998	0.997	0.996

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.847	0.491	0.846	0.519
batch 2	0.86	0.743	0.835	0.555

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	C2H2 zinc finger factors {2.3} (TFClass)
TF family	Three-zinc finger Kruppel-related {2.3.1} (TFClass)
TF subfamily	EGR {2.3.1.3} (TFClass)
TFClass ID	TFClass: 2.3.1.3.3
HGNC	HGNC:3240
MGI	MGI:1306780
EntrezGene (human)	GeneID:1960 (SSTAR profile)
EntrezGene (mouse)	GeneID:13655 (SSTAR profile)
UniProt ID (human)	EGR3_HUMAN
UniProt ID (mouse)	EGR3_MOUSE
UniProt AC (human)	Q06889 (TFClass)
UniProt AC (mouse)	P43300 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	5
Methyl-HT-SELEX	1

PCM	EGR3.H12RSNP.0.PSM.A.pcm
PWM	EGR3.H12RSNP.0.PSM.A.pwm
PFM	EGR3.H12RSNP.0.PSM.A.pfm
Alignment	EGR3.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	EGR3.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	EGR3.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	EGR3.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	EGR3.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	EGR3.H12RSNP.0.PSM.A_homer_format_0.001.txt EGR3.H12RSNP.0.PSM.A_homer_format_0.0005.txt EGR3.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	872.75	1160.75	908.75	3000.75
02	852.25	707.25	3634.25	749.25
03	379.0	4833.0	417.0	314.0
04	244.0	85.0	5439.0	175.0
05	167.0	22.0	971.0	4783.0
06	247.0	7.0	5640.0	49.0
07	20.0	19.0	5702.0	202.0
08	20.0	2.0	5885.0	36.0
09	304.0	5306.0	108.0	225.0
10	160.0	61.0	5595.0	127.0
11	302.0	127.0	2020.0	3494.0
12	1858.75	540.75	2163.75	1379.75
13	1542.75	899.75	2151.75	1348.75

PFM

	A	C	G	T
01	0.147	0.195	0.153	0.505
02	0.143	0.119	0.612	0.126
03	0.064	0.813	0.07	0.053
04	0.041	0.014	0.915	0.029
05	0.028	0.004	0.163	0.805
06	0.042	0.001	0.949	0.008
07	0.003	0.003	0.959	0.034
08	0.003	0.0	0.99	0.006
09	0.051	0.893	0.018	0.038
10	0.027	0.01	0.941	0.021
11	0.051	0.021	0.34	0.588
12	0.313	0.091	0.364	0.232
13	0.26	0.151	0.362	0.227

PWM

	A	C	G	T
01	-0.531	-0.246	-0.491	0.702
02	-0.555	-0.741	0.894	-0.683
03	-1.362	1.179	-1.267	-1.549
04	-1.799	-2.837	1.297	-2.128
05	-2.174	-4.12	-0.425	1.168
06	-1.787	-5.089	1.333	-3.37
07	-4.206	-4.252	1.344	-1.986
08	-4.206	-5.877	1.375	-3.663
09	-1.581	1.272	-2.603	-1.879
10	-2.216	-3.159	1.325	-2.444
11	-1.588	-2.444	0.307	0.854
12	0.224	-1.008	0.375	-0.074
13	0.038	-0.501	0.37	-0.097

Standard thresholds

P-value	Threshold
0.001	3.52151
0.0005	4.62046
0.0001	6.93647