EGR2.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	EGR2.H12INVIVO.0.PSM.A
Gene (human)	EGR2 (GeneCards)
Gene synonyms (human)	KROX20
Gene (mouse)	Egr2
Gene synonyms (mouse)	Egr-2, Krox-20, Zfp-25
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	14
Consensus	nbGCGTGGGCGKnn
GC content	67.65%
Information content (bits; total / per base)	14.55 / 1.039
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	8704

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	3 (16)	0.886	0.926	0.749	0.838	0.91	0.961	3.469	4.51	95.634	353.796
Mouse	9 (54)	0.844	0.949	0.77	0.893	0.862	0.96	3.365	4.478	67.358	318.268

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.989	0.986	0.859	0.876	0.69	0.743
Overall, 6 experiments	best	1.0	1.0	0.999	0.999	0.866	0.887
Methyl HT-SELEX, 1 experiments	median	0.999	0.998	0.995	0.993	0.866	0.887
Methyl HT-SELEX, 1 experiments	best	0.999	0.998	0.995	0.993	0.866	0.887
Non-Methyl HT-SELEX, 5 experiments	median	0.981	0.98	0.738	0.778	0.597	0.653
Non-Methyl HT-SELEX, 5 experiments	best	1.0	1.0	0.999	0.999	0.804	0.834

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.139	2.146	0.082	0.061

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.983	0.943	0.899	0.586

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: 2.3.1.3.2
HGNC	HGNC:3239
MGI	MGI:95296
EntrezGene (human)	GeneID:1959 (SSTAR profile)
EntrezGene (mouse)	GeneID:13654 (SSTAR profile)
UniProt ID (human)	EGR2_HUMAN
UniProt ID (mouse)	EGR2_MOUSE
UniProt AC (human)	P11161 (TFClass)
UniProt AC (mouse)	P08152 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 9 mouse
HT-SELEX	5
Methyl-HT-SELEX	1

PCM	EGR2.H12INVIVO.0.PSM.A.pcm
PWM	EGR2.H12INVIVO.0.PSM.A.pwm
PFM	EGR2.H12INVIVO.0.PSM.A.pfm
Alignment	EGR2.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	EGR2.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	EGR2.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	EGR2.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	EGR2.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	EGR2.H12INVIVO.0.PSM.A_homer_format_0.001.txt EGR2.H12INVIVO.0.PSM.A_homer_format_0.0005.txt EGR2.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2314.25	1265.25	2831.25	2293.25
02	1351.75	1483.75	1526.75	4341.75
03	826.0	179.0	7441.0	258.0
04	473.0	7459.0	219.0	553.0
05	66.0	67.0	8472.0	99.0
06	41.0	5.0	322.0	8336.0
07	851.0	1.0	7844.0	8.0
08	23.0	12.0	8640.0	29.0
09	82.0	56.0	8479.0	87.0
10	536.0	7019.0	166.0	983.0
11	265.0	200.0	7959.0	280.0
12	546.0	353.0	2764.0	5041.0
13	2224.25	1289.25	2381.25	2809.25
14	1958.0	1713.0	2287.0	2746.0

PFM

	A	C	G	T
01	0.266	0.145	0.325	0.263
02	0.155	0.17	0.175	0.499
03	0.095	0.021	0.855	0.03
04	0.054	0.857	0.025	0.064
05	0.008	0.008	0.973	0.011
06	0.005	0.001	0.037	0.958
07	0.098	0.0	0.901	0.001
08	0.003	0.001	0.993	0.003
09	0.009	0.006	0.974	0.01
10	0.062	0.806	0.019	0.113
11	0.03	0.023	0.914	0.032
12	0.063	0.041	0.318	0.579
13	0.256	0.148	0.274	0.323
14	0.225	0.197	0.263	0.315

PWM

	A	C	G	T
01	0.062	-0.541	0.263	0.052
02	-0.475	-0.382	-0.354	0.69
03	-0.967	-2.486	1.229	-2.125
04	-1.522	1.231	-2.287	-1.367
05	-3.463	-3.448	1.359	-3.069
06	-3.919	-5.703	-1.905	1.342
07	-0.937	-6.502	1.282	-5.357
08	-4.457	-5.028	1.378	-4.244
09	-3.252	-3.621	1.359	-3.195
10	-1.398	1.17	-2.561	-0.793
11	-2.098	-2.377	1.296	-2.043
12	-1.38	-1.813	0.239	0.84
13	0.022	-0.523	0.09	0.255
14	-0.105	-0.239	0.05	0.232

Standard thresholds

P-value	Threshold
0.001	2.82461
0.0005	4.06501
0.0001	6.61287