EGR1.H12INVITRO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	EGR1.H12INVITRO.0.PS.A
Gene (human)	EGR1 (GeneCards)
Gene synonyms (human)	KROX24, ZNF225
Gene (mouse)	Egr1
Gene synonyms (mouse)	Egr-1, Krox-24
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	nYGCGTGGGCGKd
GC content	72.0%
Information content (bits; total / per base)	17.409 / 1.339
Data sources	ChIP-Seq + HT-SELEX
Aligned words	2258

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	18 (118)	0.903	0.95	0.842	0.9	0.91	0.954	3.804	4.236	354.863	656.699
Mouse	4 (25)	0.895	0.951	0.762	0.887	0.868	0.948	3.107	3.974	182.0	281.585

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 5 experiments	median	0.917	0.911	0.721	0.74	0.605	0.639
Non-Methyl HT-SELEX, 5 experiments	best	0.998	0.997	0.983	0.974	0.96	0.946

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.083	27.22	0.292	0.124

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.959	0.746	0.95	0.575
batch 2	0.883	0.556	0.884	0.619

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: 2.3.1.3.1
HGNC	HGNC:3238
MGI	MGI:95295
EntrezGene (human)	GeneID:1958 (SSTAR profile)
EntrezGene (mouse)	GeneID:13653 (SSTAR profile)
UniProt ID (human)	EGR1_HUMAN
UniProt ID (mouse)	EGR1_MOUSE
UniProt AC (human)	P18146 (TFClass)
UniProt AC (mouse)	P08046 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	18 human, 4 mouse
HT-SELEX	5
Methyl-HT-SELEX	0

PCM	EGR1.H12INVITRO.0.PS.A.pcm
PWM	EGR1.H12INVITRO.0.PS.A.pwm
PFM	EGR1.H12INVITRO.0.PS.A.pfm
Alignment	EGR1.H12INVITRO.0.PS.A.words.tsv
Threshold to P-value map	EGR1.H12INVITRO.0.PS.A.thr
Motif in other formats
JASPAR format	EGR1.H12INVITRO.0.PS.A_jaspar_format.txt
MEME format	EGR1.H12INVITRO.0.PS.A_meme_format.meme
Transfac format	EGR1.H12INVITRO.0.PS.A_transfac_format.txt
Homer format	EGR1.H12INVITRO.0.PS.A_homer_format_0.001.txt EGR1.H12INVITRO.0.PS.A_homer_format_0.0005.txt EGR1.H12INVITRO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	624.0	396.0	646.0	592.0
02	213.0	356.0	197.0	1492.0
03	98.0	34.0	2109.0	17.0
04	11.0	2226.0	5.0	16.0
05	0.0	0.0	2258.0	0.0
06	0.0	0.0	42.0	2216.0
07	2.0	0.0	2256.0	0.0
08	0.0	0.0	2258.0	0.0
09	0.0	0.0	2257.0	1.0
10	84.0	1946.0	21.0	207.0
11	58.0	11.0	2158.0	31.0
12	188.75	94.75	845.75	1128.75
13	748.25	238.25	780.25	491.25

PFM

	A	C	G	T
01	0.276	0.175	0.286	0.262
02	0.094	0.158	0.087	0.661
03	0.043	0.015	0.934	0.008
04	0.005	0.986	0.002	0.007
05	0.0	0.0	1.0	0.0
06	0.0	0.0	0.019	0.981
07	0.001	0.0	0.999	0.0
08	0.0	0.0	1.0	0.0
09	0.0	0.0	1.0	0.0
10	0.037	0.862	0.009	0.092
11	0.026	0.005	0.956	0.014
12	0.084	0.042	0.375	0.5
13	0.331	0.106	0.346	0.218

PWM

	A	C	G	T
01	0.1	-0.353	0.134	0.047
02	-0.969	-0.459	-1.046	0.97
03	-1.735	-2.758	1.316	-3.399
04	-3.78	1.369	-4.403	-3.453
05	-5.682	-5.682	1.384	-5.682
06	-5.682	-5.682	-2.557	1.365
07	-4.971	-5.682	1.383	-5.682
08	-5.682	-5.682	1.384	-5.682
09	-5.682	-5.682	1.383	-5.264
10	-1.886	1.235	-3.207	-0.997
11	-2.246	-3.78	1.338	-2.845
12	-1.089	-1.768	0.403	0.691
13	0.281	-0.858	0.323	-0.138

Standard thresholds

P-value	Threshold
0.001	-0.18884
0.0005	1.47901
0.0001	4.97131