EGR3.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	EGR3.H12INVIVO.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	nShGKGGGMGKvd
GC content	69.63%
Information content (bits; total / per base)	9.985 / 0.768
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	953

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)	0.869	0.928	0.708	0.826	0.899	0.9	3.113	3.13	102.237	169.108

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.624	0.609	0.553	0.557	0.526	0.533
Overall, 6 experiments	best	0.947	0.894	0.948	0.901	0.934	0.89
Methyl HT-SELEX, 1 experiments	median	0.907	0.855	0.774	0.755	0.621	0.648
Methyl HT-SELEX, 1 experiments	best	0.907	0.855	0.774	0.755	0.621	0.648
Non-Methyl HT-SELEX, 5 experiments	median	0.601	0.584	0.543	0.544	0.522	0.525
Non-Methyl HT-SELEX, 5 experiments	best	0.947	0.894	0.948	0.901	0.934	0.89

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.656	0.27	0.671	0.438
batch 2	0.669	0.364	0.725	0.435

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.H12INVIVO.0.PSM.A.pcm
PWM	EGR3.H12INVIVO.0.PSM.A.pwm
PFM	EGR3.H12INVIVO.0.PSM.A.pfm
Alignment	EGR3.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	EGR3.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	EGR3.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	EGR3.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	EGR3.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	EGR3.H12INVIVO.0.PSM.A_homer_format_0.001.txt EGR3.H12INVIVO.0.PSM.A_homer_format_0.0005.txt EGR3.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	156.0	182.0	360.0	255.0
02	100.0	181.0	602.0	70.0
03	282.0	236.0	100.0	335.0
04	23.0	28.0	891.0	11.0
05	59.0	45.0	419.0	430.0
06	224.0	10.0	712.0	7.0
07	1.0	2.0	928.0	22.0
08	8.0	10.0	928.0	7.0
09	372.0	312.0	1.0	268.0
10	96.0	9.0	786.0	62.0
11	58.0	62.0	675.0	158.0
12	273.0	195.0	351.0	134.0
13	178.0	120.0	482.0	173.0

PFM

	A	C	G	T
01	0.164	0.191	0.378	0.268
02	0.105	0.19	0.632	0.073
03	0.296	0.248	0.105	0.352
04	0.024	0.029	0.935	0.012
05	0.062	0.047	0.44	0.451
06	0.235	0.01	0.747	0.007
07	0.001	0.002	0.974	0.023
08	0.008	0.01	0.974	0.007
09	0.39	0.327	0.001	0.281
10	0.101	0.009	0.825	0.065
11	0.061	0.065	0.708	0.166
12	0.286	0.205	0.368	0.141
13	0.187	0.126	0.506	0.182

PWM

	A	C	G	T
01	-0.42	-0.267	0.41	0.067
02	-0.858	-0.273	0.923	-1.208
03	0.167	-0.009	-0.858	0.339
04	-2.273	-2.089	1.314	-2.938
05	-1.374	-1.636	0.561	0.587
06	-0.061	-3.02	1.09	-3.315
07	-4.482	-4.168	1.354	-2.314
08	-3.207	-3.02	1.354	-3.315
09	0.443	0.268	-4.482	0.117
10	-0.898	-3.109	1.189	-1.326
11	-1.391	-1.326	1.037	-0.407
12	0.135	-0.199	0.385	-0.57
13	-0.289	-0.679	0.701	-0.317

Standard thresholds

P-value	Threshold
0.001	4.77761
0.0005	5.65061
0.0001	7.36976