HME1.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HME1.H12INVIVO.0.PSM.A
Gene (human)	EN1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	En1
Gene synonyms (mouse)	En-1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	nbYAATTARbnn
GC content	33.66%
Information content (bits; total / per base)	11.507 / 0.959
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	7278

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 (2)	0.708	0.708	0.604	0.604	0.716	0.716	2.121	2.121	12.658	12.658

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.927	0.9	0.794	0.78	0.664	0.677
Overall, 6 experiments	best	0.957	0.929	0.935	0.901	0.883	0.844
Methyl HT-SELEX, 1 experiments	median	0.957	0.929	0.935	0.901	0.877	0.844
Methyl HT-SELEX, 1 experiments	best	0.957	0.929	0.935	0.901	0.877	0.844
Non-Methyl HT-SELEX, 5 experiments	median	0.921	0.893	0.787	0.773	0.66	0.673
Non-Methyl HT-SELEX, 5 experiments	best	0.949	0.917	0.928	0.889	0.883	0.844

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	EN {3.1.2.7} (TFClass)
TFClass ID	TFClass: 3.1.2.7.1
HGNC	HGNC:3342
MGI	MGI:95389
EntrezGene (human)	GeneID:2019 (SSTAR profile)
EntrezGene (mouse)	GeneID:13798 (SSTAR profile)
UniProt ID (human)	HME1_HUMAN
UniProt ID (mouse)	HME1_MOUSE
UniProt AC (human)	Q05925 (TFClass)
UniProt AC (mouse)	P09065 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	5
Methyl-HT-SELEX	1

PCM	HME1.H12INVIVO.0.PSM.A.pcm
PWM	HME1.H12INVIVO.0.PSM.A.pwm
PFM	HME1.H12INVIVO.0.PSM.A.pfm
Alignment	HME1.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	HME1.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	HME1.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	HME1.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	HME1.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	HME1.H12INVIVO.0.PSM.A_homer_format_0.001.txt HME1.H12INVIVO.0.PSM.A_homer_format_0.0005.txt HME1.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1918.0	1551.0	2245.0	1564.0
02	1054.25	1744.25	2969.25	1510.25
03	111.0	2973.0	99.0	4095.0
04	7091.0	56.0	131.0	0.0
05	7278.0	0.0	0.0	0.0
06	0.0	0.0	0.0	7278.0
07	0.0	0.0	0.0	7278.0
08	7278.0	0.0	0.0	0.0
09	1879.0	749.0	4342.0	308.0
10	703.0	3127.0	1474.0	1974.0
11	1858.25	2141.25	2096.25	1182.25
12	1975.5	2261.5	1438.5	1602.5

PFM

	A	C	G	T
01	0.264	0.213	0.308	0.215
02	0.145	0.24	0.408	0.208
03	0.015	0.408	0.014	0.563
04	0.974	0.008	0.018	0.0
05	1.0	0.0	0.0	0.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	0.0	1.0
08	1.0	0.0	0.0	0.0
09	0.258	0.103	0.597	0.042
10	0.097	0.43	0.203	0.271
11	0.255	0.294	0.288	0.162
12	0.271	0.311	0.198	0.22

PWM

	A	C	G	T
01	0.053	-0.159	0.21	-0.151
02	-0.545	-0.042	0.489	-0.186
03	-2.778	0.491	-2.89	0.811
04	1.359	-3.443	-2.616	-6.709
05	1.385	-6.709	-6.709	-6.709
06	-6.709	-6.709	-6.709	1.385
07	-6.709	-6.709	-6.709	1.385
08	1.385	-6.709	-6.709	-6.709
09	0.032	-0.886	0.869	-1.77
10	-0.949	0.541	-0.21	0.081
11	0.021	0.163	0.141	-0.43
12	0.082	0.217	-0.235	-0.127

Standard thresholds

P-value	Threshold
0.001	3.355325
0.0005	5.109985
0.0001	7.97526