EGR2.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	EGR2.H12RSNP.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	15
Consensus	ndbGCGTGGGCGKdn
GC content	69.96%
Information content (bits; total / per base)	18.25 / 1.217
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	7619

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)	0.852	0.894	0.741	0.818	0.904	0.953	3.286	4.397	88.151	319.796
Mouse	9 (54)	0.804	0.889	0.736	0.846	0.852	0.963	3.312	4.632	57.845	301.174

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.974	0.972	0.844	0.861	0.664	0.718
Overall, 6 experiments	best	1.0	0.999	0.993	0.991	0.846	0.869
Methyl HT-SELEX, 1 experiments	median	0.999	0.998	0.993	0.991	0.846	0.869
Methyl HT-SELEX, 1 experiments	best	0.999	0.998	0.993	0.991	0.846	0.869
Non-Methyl HT-SELEX, 5 experiments	median	0.953	0.952	0.711	0.75	0.587	0.638
Non-Methyl HT-SELEX, 5 experiments	best	1.0	0.999	0.98	0.981	0.811	0.834

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.211	2.23	0.106	0.065

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.984	0.944	0.891	0.572

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.H12RSNP.0.PSM.A.pcm
PWM	EGR2.H12RSNP.0.PSM.A.pwm
PFM	EGR2.H12RSNP.0.PSM.A.pfm
Alignment	EGR2.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	EGR2.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	EGR2.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	EGR2.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	EGR2.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	EGR2.H12RSNP.0.PSM.A_homer_format_0.001.txt EGR2.H12RSNP.0.PSM.A_homer_format_0.0005.txt EGR2.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2054.25	1388.25	2085.25	2091.25
02	2328.25	787.25	2534.25	1969.25
03	1097.0	1568.0	1418.0	3536.0
04	382.0	29.0	7181.0	27.0
05	52.0	7489.0	16.0	62.0
06	0.0	0.0	7619.0	0.0
07	0.0	0.0	0.0	7619.0
08	67.0	0.0	7552.0	0.0
09	0.0	0.0	7619.0	0.0
10	0.0	0.0	7619.0	0.0
11	114.0	7351.0	1.0	153.0
12	21.0	2.0	7590.0	6.0
13	613.0	195.0	2214.0	4597.0
14	2264.5	695.5	3050.5	1608.5
15	2092.25	1248.25	2701.25	1577.25

PFM

	A	C	G	T
01	0.27	0.182	0.274	0.274
02	0.306	0.103	0.333	0.258
03	0.144	0.206	0.186	0.464
04	0.05	0.004	0.943	0.004
05	0.007	0.983	0.002	0.008
06	0.0	0.0	1.0	0.0
07	0.0	0.0	0.0	1.0
08	0.009	0.0	0.991	0.0
09	0.0	0.0	1.0	0.0
10	0.0	0.0	1.0	0.0
11	0.015	0.965	0.0	0.02
12	0.003	0.0	0.996	0.001
13	0.08	0.026	0.291	0.603
14	0.297	0.091	0.4	0.211
15	0.275	0.164	0.355	0.207

PWM

	A	C	G	T
01	0.075	-0.316	0.09	0.093
02	0.201	-0.882	0.285	0.033
03	-0.551	-0.194	-0.295	0.618
04	-1.602	-4.112	1.326	-4.178
05	-3.56	1.368	-4.65	-3.391
06	-6.749	-6.749	1.385	-6.749
07	-6.749	-6.749	-6.749	1.385
08	-3.316	-6.749	1.377	-6.749
09	-6.749	-6.749	1.385	-6.749
10	-6.749	-6.749	1.385	-6.749
11	-2.798	1.35	-6.379	-2.508
12	-4.408	-6.11	1.382	-5.445
13	-1.131	-2.269	0.15	0.88
14	0.173	-1.005	0.471	-0.169
15	0.094	-0.422	0.349	-0.188

Standard thresholds

P-value	Threshold
0.001	-2.78999
0.0005	-0.76014
0.0001	3.49471