LHX4.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX4.H12INVIVO.0.SM.D
Gene (human)	LHX4 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lhx4
Gene synonyms (mouse)	Gsh-4, Gsh4
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	12
Consensus	nbYAATTARbnn
GC content	30.5%
Information content (bits; total / per base)	11.529 / 0.961
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8107

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.945	0.911	0.912	0.874	0.828	0.8
Overall, 6 experiments	best	0.98	0.968	0.956	0.938	0.85	0.845
Methyl HT-SELEX, 2 experiments	median	0.962	0.94	0.93	0.901	0.84	0.82
Methyl HT-SELEX, 2 experiments	best	0.962	0.941	0.931	0.901	0.845	0.822
Non-Methyl HT-SELEX, 4 experiments	median	0.802	0.77	0.736	0.715	0.676	0.665
Non-Methyl HT-SELEX, 4 experiments	best	0.98	0.968	0.956	0.938	0.85	0.845

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.802	0.633	0.824	0.628

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HD-LIM {3.1.5} (TFClass)
TF subfamily	LHX3-like {3.1.5.4} (TFClass)
TFClass ID	TFClass: 3.1.5.4.2
HGNC	HGNC:21734
MGI	MGI:101776
EntrezGene (human)	GeneID:89884 (SSTAR profile)
EntrezGene (mouse)	GeneID:16872 (SSTAR profile)
UniProt ID (human)	LHX4_HUMAN
UniProt ID (mouse)	LHX4_MOUSE
UniProt AC (human)	Q969G2 (TFClass)
UniProt AC (mouse)	P53776 (TFClass)
GRECO-DB-TF	yes

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

PCM	LHX4.H12INVIVO.0.SM.D.pcm
PWM	LHX4.H12INVIVO.0.SM.D.pwm
PFM	LHX4.H12INVIVO.0.SM.D.pfm
Alignment	LHX4.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	LHX4.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	LHX4.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	LHX4.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	LHX4.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	LHX4.H12INVIVO.0.SM.D_homer_format_0.001.txt LHX4.H12INVIVO.0.SM.D_homer_format_0.0005.txt LHX4.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1846.0	2156.0	1961.0	2144.0
02	1060.75	2384.75	3071.75	1589.75
03	164.0	2181.0	78.0	5684.0
04	7396.0	21.0	690.0	0.0
05	8107.0	0.0	0.0	0.0
06	0.0	0.0	0.0	8107.0
07	0.0	0.0	0.0	8107.0
08	8107.0	0.0	0.0	0.0
09	4186.0	914.0	2954.0	53.0
10	380.0	3008.0	1512.0	3207.0
11	1413.75	1976.75	2904.75	1811.75
12	2374.0	1983.0	1871.0	1879.0

PFM

	A	C	G	T
01	0.228	0.266	0.242	0.264
02	0.131	0.294	0.379	0.196
03	0.02	0.269	0.01	0.701
04	0.912	0.003	0.085	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	0.516	0.113	0.364	0.007
10	0.047	0.371	0.187	0.396
11	0.174	0.244	0.358	0.223
12	0.293	0.245	0.231	0.232

PWM

	A	C	G	T
01	-0.093	0.062	-0.033	0.056
02	-0.646	0.162	0.415	-0.243
03	-2.502	0.073	-3.23	1.031
04	1.294	-4.469	-1.075	-6.804
05	1.385	-6.804	-6.804	-6.804
06	-6.804	-6.804	-6.804	1.385
07	-6.804	-6.804	-6.804	1.385
08	1.385	-6.804	-6.804	-6.804
09	0.725	-0.795	0.376	-3.603
10	-1.669	0.394	-0.293	0.458
11	-0.36	-0.025	0.36	-0.112
12	0.158	-0.022	-0.08	-0.076

Standard thresholds

P-value	Threshold
0.001	3.350265
0.0005	5.276935
0.0001	7.96596