EMX1.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	EMX1.H12INVIVO.0.SM.D
Gene (human)	EMX1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Emx1
Gene synonyms (mouse)	Emx-1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	13
Consensus	nnbTMATTARbnn
GC content	36.4%
Information content (bits; total / per base)	11.514 / 0.886
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9080

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.98	0.968	0.965	0.944	0.944	0.918
Overall, 6 experiments	best	0.994	0.991	0.988	0.982	0.972	0.961
Methyl HT-SELEX, 2 experiments	median	0.982	0.97	0.972	0.956	0.954	0.933
Methyl HT-SELEX, 2 experiments	best	0.994	0.99	0.988	0.982	0.972	0.961
Non-Methyl HT-SELEX, 4 experiments	median	0.98	0.968	0.948	0.931	0.858	0.854
Non-Methyl HT-SELEX, 4 experiments	best	0.994	0.991	0.988	0.982	0.966	0.956

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.977	0.803	0.928	0.491
batch 2	0.712	0.539	0.666	0.429

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.H12INVIVO.0.SM.D.pcm
PWM	EMX1.H12INVIVO.0.SM.D.pwm
PFM	EMX1.H12INVIVO.0.SM.D.pfm
Alignment	EMX1.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	EMX1.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	EMX1.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	EMX1.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	EMX1.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	EMX1.H12INVIVO.0.SM.D_homer_format_0.001.txt EMX1.H12INVIVO.0.SM.D_homer_format_0.0005.txt EMX1.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2384.75	1906.75	2632.75	2155.75
02	1588.0	2914.0	2864.0	1714.0
03	1196.0	2972.0	3625.0	1287.0
04	165.0	1352.0	33.0	7530.0
05	5493.0	3478.0	96.0	13.0
06	9080.0	0.0	0.0	0.0
07	0.0	0.0	0.0	9080.0
08	0.0	0.0	0.0	9080.0
09	9080.0	0.0	0.0	0.0
10	2706.0	549.0	5741.0	84.0
11	417.0	3558.0	1921.0	3184.0
12	1516.5	1804.5	3524.5	2234.5
13	2681.25	2215.25	1778.25	2405.25

PFM

	A	C	G	T
01	0.263	0.21	0.29	0.237
02	0.175	0.321	0.315	0.189
03	0.132	0.327	0.399	0.142
04	0.018	0.149	0.004	0.829
05	0.605	0.383	0.011	0.001
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	0.298	0.06	0.632	0.009
11	0.046	0.392	0.212	0.351
12	0.167	0.199	0.388	0.246
13	0.295	0.244	0.196	0.265

PWM

	A	C	G	T
01	0.049	-0.174	0.148	-0.052
02	-0.357	0.25	0.232	-0.281
03	-0.64	0.269	0.468	-0.567
04	-2.609	-0.518	-4.165	1.198
05	0.883	0.426	-3.141	-5.002
06	1.386	-6.905	-6.905	-6.905
07	-6.905	-6.905	-6.905	1.386
08	-6.905	-6.905	-6.905	1.386
09	1.386	-6.905	-6.905	-6.905
10	0.176	-1.416	0.927	-3.271
11	-1.69	0.449	-0.167	0.338
12	-0.403	-0.229	0.44	-0.016
13	0.166	-0.024	-0.244	0.058

Standard thresholds

P-value	Threshold
0.001	3.54116
0.0005	5.323965
0.0001	7.88416