EGR2.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	EGR2.H12INVITRO.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	13
Consensus	nhGCGTGGGYGdd
GC content	70.24%
Information content (bits; total / per base)	13.713 / 1.055
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	6622

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)	0.868	0.909	0.725	0.805	0.91	0.945	3.57	4.349	87.891	311.538
Mouse	9 (54)	0.819	0.925	0.739	0.852	0.852	0.944	3.253	4.265	61.577	294.0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.984	0.981	0.856	0.87	0.695	0.742
Overall, 6 experiments	best	1.0	0.999	0.997	0.997	0.867	0.884
Methyl HT-SELEX, 1 experiments	median	0.999	0.998	0.992	0.989	0.867	0.884
Methyl HT-SELEX, 1 experiments	best	0.999	0.998	0.992	0.989	0.867	0.884
Non-Methyl HT-SELEX, 5 experiments	median	0.974	0.971	0.742	0.776	0.604	0.655
Non-Methyl HT-SELEX, 5 experiments	best	1.0	0.999	0.997	0.997	0.81	0.835

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	1.913	1.665	0.072	0.056

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.949	0.92	0.884	0.546

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.H12INVITRO.0.PSM.A.pcm
PWM	EGR2.H12INVITRO.0.PSM.A.pwm
PFM	EGR2.H12INVITRO.0.PSM.A.pfm
Alignment	EGR2.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	EGR2.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	EGR2.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	EGR2.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	EGR2.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	EGR2.H12INVITRO.0.PSM.A_homer_format_0.001.txt EGR2.H12INVITRO.0.PSM.A_homer_format_0.0005.txt EGR2.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1563.75	1127.75	2317.75	1612.75
02	994.0	1163.0	841.0	3624.0
03	516.0	211.0	5603.0	292.0
04	283.0	5459.0	541.0	339.0
05	15.0	1.0	6600.0	6.0
06	3.0	0.0	74.0	6545.0
07	279.0	2.0	6339.0	2.0
08	71.0	45.0	6395.0	111.0
09	175.0	49.0	6212.0	186.0
10	940.0	4254.0	448.0	980.0
11	488.0	111.0	5727.0	296.0
12	690.0	421.0	3022.0	2489.0
13	1541.0	826.0	2678.0	1577.0

PFM

	A	C	G	T
01	0.236	0.17	0.35	0.244
02	0.15	0.176	0.127	0.547
03	0.078	0.032	0.846	0.044
04	0.043	0.824	0.082	0.051
05	0.002	0.0	0.997	0.001
06	0.0	0.0	0.011	0.988
07	0.042	0.0	0.957	0.0
08	0.011	0.007	0.966	0.017
09	0.026	0.007	0.938	0.028
10	0.142	0.642	0.068	0.148
11	0.074	0.017	0.865	0.045
12	0.104	0.064	0.456	0.376
13	0.233	0.125	0.404	0.238

PWM

	A	C	G	T
01	-0.057	-0.383	0.336	-0.026
02	-0.509	-0.353	-0.676	0.783
03	-1.163	-2.051	1.218	-1.729
04	-1.76	1.192	-1.116	-1.581
05	-4.568	-6.25	1.382	-5.309
06	-5.765	-6.625	-3.08	1.374
07	-1.774	-5.978	1.342	-5.978
08	-3.12	-3.559	1.35	-2.684
09	-2.236	-3.477	1.321	-2.176
10	-0.565	0.943	-1.303	-0.523
11	-1.218	-2.684	1.24	-1.715
12	-0.873	-1.365	0.601	0.407
13	-0.072	-0.694	0.48	-0.049

Standard thresholds

P-value	Threshold
0.001	3.26241
0.0005	4.45931
0.0001	6.902345