ELK3.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	ELK3.H12RSNP.0.PSM.A
Gene (human)	ELK3 (GeneCards)
Gene synonyms (human)	NET, SAP2
Gene (mouse)	Elk3
Gene synonyms (mouse)	Erp, Net
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	nnACCGGAAGTdn
GC content	53.62%
Information content (bits; total / per base)	16.894 / 1.3
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9904

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 (7)	0.94	0.952	0.908	0.92	0.91	0.916	3.853	3.922	226.658	256.009

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.997	0.996	0.992	0.989	0.945	0.941
Overall, 10 experiments	best	0.999	0.998	0.997	0.996	0.994	0.991
Methyl HT-SELEX, 3 experiments	median	0.998	0.997	0.997	0.995	0.983	0.98
Methyl HT-SELEX, 3 experiments	best	0.999	0.998	0.997	0.995	0.989	0.986
Non-Methyl HT-SELEX, 7 experiments	median	0.966	0.961	0.794	0.804	0.647	0.681
Non-Methyl HT-SELEX, 7 experiments	best	0.999	0.998	0.997	0.996	0.994	0.991

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.992	0.96	0.975	0.688
batch 2	0.875	0.722	0.865	0.709

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Tryptophan cluster factors {3.5} (TFClass)
TF family	Ets-related {3.5.2} (TFClass)
TF subfamily	ELK-like {3.5.2.2} (TFClass)
TFClass ID	TFClass: 3.5.2.2.2
HGNC	HGNC:3325
MGI	MGI:101762
EntrezGene (human)	GeneID:2004 (SSTAR profile)
EntrezGene (mouse)	GeneID:13713 (SSTAR profile)
UniProt ID (human)	ELK3_HUMAN
UniProt ID (mouse)	ELK3_MOUSE
UniProt AC (human)	P41970 (TFClass)
UniProt AC (mouse)	P41971 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	7
Methyl-HT-SELEX	3

PCM	ELK3.H12RSNP.0.PSM.A.pcm
PWM	ELK3.H12RSNP.0.PSM.A.pwm
PFM	ELK3.H12RSNP.0.PSM.A.pfm
Alignment	ELK3.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	ELK3.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	ELK3.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	ELK3.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	ELK3.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	ELK3.H12RSNP.0.PSM.A_homer_format_0.001.txt ELK3.H12RSNP.0.PSM.A_homer_format_0.0005.txt ELK3.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2867.0	2061.0	2632.0	2344.0
02	3791.0	2061.0	2408.0	1644.0
03	8287.0	45.0	881.0	691.0
04	20.0	9815.0	63.0	6.0
05	2.0	9902.0	0.0	0.0
06	0.0	0.0	9904.0	0.0
07	0.0	0.0	9904.0	0.0
08	9904.0	0.0	0.0	0.0
09	9883.0	1.0	0.0	20.0
10	82.0	29.0	9793.0	0.0
11	49.0	401.0	28.0	9426.0
12	3364.0	1029.0	3226.0	2285.0
13	3421.75	2351.75	2500.75	1629.75

PFM

	A	C	G	T
01	0.289	0.208	0.266	0.237
02	0.383	0.208	0.243	0.166
03	0.837	0.005	0.089	0.07
04	0.002	0.991	0.006	0.001
05	0.0	1.0	0.0	0.0
06	0.0	0.0	1.0	0.0
07	0.0	0.0	1.0	0.0
08	1.0	0.0	0.0	0.0
09	0.998	0.0	0.0	0.002
10	0.008	0.003	0.989	0.0
11	0.005	0.04	0.003	0.952
12	0.34	0.104	0.326	0.231
13	0.345	0.237	0.252	0.165

PWM

	A	C	G	T
01	0.146	-0.183	0.061	-0.055
02	0.426	-0.183	-0.028	-0.409
03	1.207	-3.959	-1.032	-1.274
04	-4.711	1.377	-3.636	-5.699
05	-6.357	1.385	-6.982	-6.982
06	-6.982	-6.982	1.386	-6.982
07	-6.982	-6.982	1.386	-6.982
08	1.386	-6.982	-6.982	-6.982
09	1.383	-6.621	-6.982	-4.711
10	-3.381	-4.372	1.374	-6.982
11	-3.878	-1.816	-4.404	1.336
12	0.306	-0.877	0.264	-0.08
13	0.323	-0.051	0.01	-0.418

Standard thresholds

P-value	Threshold
0.001	-1.924235
0.0005	-0.025585
0.0001	4.212915