EGR3.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	EGR3.H12INVITRO.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	14
Consensus	ndhGCGTGGGMGKd
GC content	66.79%
Information content (bits; total / per base)	13.392 / 0.957
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1396

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)	0.841	0.888	0.697	0.772	0.834	0.838	2.631	2.66	82.509	142.06

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.664	0.679	0.578	0.593	0.541	0.554
Overall, 6 experiments	best	0.999	0.999	0.999	0.998	0.996	0.995
Methyl HT-SELEX, 1 experiments	median	0.984	0.981	0.816	0.83	0.651	0.694
Methyl HT-SELEX, 1 experiments	best	0.984	0.981	0.816	0.83	0.651	0.694
Non-Methyl HT-SELEX, 5 experiments	median	0.63	0.642	0.563	0.574	0.535	0.543
Non-Methyl HT-SELEX, 5 experiments	best	0.999	0.999	0.999	0.998	0.996	0.995

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.839	0.512	0.849	0.59
batch 2	0.84	0.604	0.816	0.491

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.H12INVITRO.0.PSM.A.pcm
PWM	EGR3.H12INVITRO.0.PSM.A.pwm
PFM	EGR3.H12INVITRO.0.PSM.A.pfm
Alignment	EGR3.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	EGR3.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	EGR3.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	EGR3.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	EGR3.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	EGR3.H12INVITRO.0.PSM.A_homer_format_0.001.txt EGR3.H12INVITRO.0.PSM.A_homer_format_0.0005.txt EGR3.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	442.5	264.5	352.5	336.5
02	431.25	171.25	463.25	330.25
03	187.0	259.0	182.0	768.0
04	147.0	14.0	1190.0	45.0
05	42.0	1152.0	151.0	51.0
06	6.0	0.0	1387.0	3.0
07	21.0	0.0	112.0	1263.0
08	20.0	0.0	1375.0	1.0
09	19.0	6.0	1337.0	34.0
10	47.0	7.0	1293.0	49.0
11	228.0	900.0	120.0	148.0
12	134.0	30.0	1130.0	102.0
13	128.75	58.75	470.75	737.75
14	354.25	155.25	471.25	415.25

PFM

	A	C	G	T
01	0.317	0.189	0.253	0.241
02	0.309	0.123	0.332	0.237
03	0.134	0.186	0.13	0.55
04	0.105	0.01	0.852	0.032
05	0.03	0.825	0.108	0.037
06	0.004	0.0	0.994	0.002
07	0.015	0.0	0.08	0.905
08	0.014	0.0	0.985	0.001
09	0.014	0.004	0.958	0.024
10	0.034	0.005	0.926	0.035
11	0.163	0.645	0.086	0.106
12	0.096	0.021	0.809	0.073
13	0.092	0.042	0.337	0.528
14	0.254	0.111	0.338	0.297

PWM

	A	C	G	T
01	0.236	-0.276	0.01	-0.036
02	0.211	-0.707	0.282	-0.055
03	-0.62	-0.296	-0.646	0.786
04	-0.858	-3.1	1.223	-2.014
05	-2.08	1.191	-0.831	-1.894
06	-3.805	-5.267	1.376	-4.289
07	-2.733	-5.267	-1.126	1.282
08	-2.778	-5.267	1.367	-4.827
09	-2.825	-3.805	1.339	-2.282
10	-1.972	-3.684	1.306	-1.932
11	-0.423	0.944	-1.058	-0.851
12	-0.949	-2.4	1.171	-1.218
13	-0.988	-1.757	0.298	0.746
14	0.015	-0.804	0.299	0.173

Standard thresholds

P-value	Threshold
0.001	3.57476
0.0005	4.68721
0.0001	6.98706