EMX1.H12RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	EMX1.H12RSNP.0.SM.B
Gene (human)	EMX1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Emx1
Gene synonyms (mouse)	Emx-1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	13
Consensus	nnbTMATTARbnn
GC content	35.68%
Information content (bits; total / per base)	11.138 / 0.857
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9231

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.98	0.968	0.964	0.943	0.943	0.917
Overall, 6 experiments	best	0.994	0.991	0.988	0.981	0.972	0.961
Methyl HT-SELEX, 2 experiments	median	0.981	0.969	0.972	0.955	0.953	0.932
Methyl HT-SELEX, 2 experiments	best	0.994	0.99	0.988	0.981	0.972	0.961
Non-Methyl HT-SELEX, 4 experiments	median	0.98	0.968	0.948	0.931	0.856	0.853
Non-Methyl HT-SELEX, 4 experiments	best	0.994	0.991	0.988	0.981	0.966	0.955

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.981	0.808	0.932	0.506
batch 2	0.714	0.544	0.666	0.436

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	NK-related {3.1.2} (TFClass)
TF subfamily	EMX {3.1.2.6} (TFClass)
TFClass ID	TFClass: 3.1.2.6.1
HGNC	HGNC:3340
MGI	MGI:95387
EntrezGene (human)	GeneID:2016 (SSTAR profile)
EntrezGene (mouse)	GeneID:13796 (SSTAR profile)
UniProt ID (human)	EMX1_HUMAN
UniProt ID (mouse)	EMX1_MOUSE
UniProt AC (human)	Q04741 (TFClass)
UniProt AC (mouse)	Q04742 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	4
Methyl-HT-SELEX	2

PCM	EMX1.H12RSNP.0.SM.B.pcm
PWM	EMX1.H12RSNP.0.SM.B.pwm
PFM	EMX1.H12RSNP.0.SM.B.pfm
Alignment	EMX1.H12RSNP.0.SM.B.words.tsv
Threshold to P-value map	EMX1.H12RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	EMX1.H12RSNP.0.SM.B_jaspar_format.txt
MEME format	EMX1.H12RSNP.0.SM.B_meme_format.meme
Transfac format	EMX1.H12RSNP.0.SM.B_transfac_format.txt
Homer format	EMX1.H12RSNP.0.SM.B_homer_format_0.001.txt EMX1.H12RSNP.0.SM.B_homer_format_0.0005.txt EMX1.H12RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2393.75	1903.75	2591.75	2341.75
02	1719.5	2837.5	2866.5	1807.5
03	1462.0	2848.0	3420.0	1501.0
04	228.0	1765.0	54.0	7184.0
05	5614.0	3369.0	175.0	73.0
06	9230.0	0.0	1.0	0.0
07	0.0	0.0	0.0	9231.0
08	0.0	0.0	0.0	9231.0
09	9231.0	0.0	0.0	0.0
10	3019.0	470.0	5620.0	122.0
11	569.0	3443.0	1919.0	3300.0
12	1547.5	1879.5	3476.5	2327.5
13	2716.75	2246.75	1928.75	2338.75

PFM

	A	C	G	T
01	0.259	0.206	0.281	0.254
02	0.186	0.307	0.311	0.196
03	0.158	0.309	0.37	0.163
04	0.025	0.191	0.006	0.778
05	0.608	0.365	0.019	0.008
06	1.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	1.0	0.0	0.0	0.0
10	0.327	0.051	0.609	0.013
11	0.062	0.373	0.208	0.357
12	0.168	0.204	0.377	0.252
13	0.294	0.243	0.209	0.253

PWM

	A	C	G	T
01	0.037	-0.192	0.116	0.015
02	-0.294	0.206	0.217	-0.244
03	-0.456	0.21	0.393	-0.43
04	-2.306	-0.268	-3.715	1.135
05	0.888	0.378	-2.567	-3.424
06	1.385	-6.92	-6.556	-6.92
07	-6.92	-6.92	-6.92	1.386
08	-6.92	-6.92	-6.92	1.386
09	1.386	-6.92	-6.92	-6.92
10	0.268	-1.587	0.889	-2.922
11	-1.397	0.4	-0.184	0.357
12	-0.399	-0.205	0.409	0.009
13	0.163	-0.027	-0.179	0.013

Standard thresholds

P-value	Threshold
0.001	4.06926
0.0005	5.55696
0.0001	7.90066