LHX4.H12RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX4.H12RSNP.0.SM.B
Gene (human)	LHX4 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lhx4
Gene synonyms (mouse)	Gsh-4, Gsh4
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	14
Consensus	nnbTAATTARYbnn
GC content	26.89%
Information content (bits; total / per base)	13.628 / 0.973
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	705

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.937	0.896	0.906	0.862	0.817	0.788
Overall, 6 experiments	best	0.972	0.951	0.951	0.926	0.839	0.833
Methyl HT-SELEX, 2 experiments	median	0.955	0.925	0.924	0.889	0.826	0.806
Methyl HT-SELEX, 2 experiments	best	0.956	0.926	0.925	0.891	0.831	0.809
Non-Methyl HT-SELEX, 4 experiments	median	0.798	0.762	0.733	0.71	0.673	0.66
Non-Methyl HT-SELEX, 4 experiments	best	0.972	0.951	0.951	0.926	0.839	0.833

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.811	0.645	0.826	0.665

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.H12RSNP.0.SM.B.pcm
PWM	LHX4.H12RSNP.0.SM.B.pwm
PFM	LHX4.H12RSNP.0.SM.B.pfm
Alignment	LHX4.H12RSNP.0.SM.B.words.tsv
Threshold to P-value map	LHX4.H12RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	LHX4.H12RSNP.0.SM.B_jaspar_format.txt
MEME format	LHX4.H12RSNP.0.SM.B_meme_format.meme
Transfac format	LHX4.H12RSNP.0.SM.B_transfac_format.txt
Homer format	LHX4.H12RSNP.0.SM.B_homer_format_0.001.txt LHX4.H12RSNP.0.SM.B_homer_format_0.0005.txt LHX4.H12RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	192.25	139.25	181.25	192.25
02	121.5	121.5	345.5	116.5
03	46.0	218.0	224.0	217.0
04	4.0	27.0	0.0	674.0
05	696.0	1.0	8.0	0.0
06	705.0	0.0	0.0	0.0
07	0.0	0.0	0.0	705.0
08	0.0	0.0	0.0	705.0
09	705.0	0.0	0.0	0.0
10	498.0	26.0	179.0	2.0
11	75.0	111.0	79.0	440.0
12	64.0	186.0	152.0	303.0
13	151.0	234.0	132.0	188.0
14	213.0	166.0	124.0	202.0

PFM

	A	C	G	T
01	0.273	0.198	0.257	0.273
02	0.172	0.172	0.49	0.165
03	0.065	0.309	0.318	0.308
04	0.006	0.038	0.0	0.956
05	0.987	0.001	0.011	0.0
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	0.706	0.037	0.254	0.003
11	0.106	0.157	0.112	0.624
12	0.091	0.264	0.216	0.43
13	0.214	0.332	0.187	0.267
14	0.302	0.235	0.176	0.287

PWM

	A	C	G	T
01	0.086	-0.233	0.028	0.086
02	-0.368	-0.368	0.669	-0.409
03	-1.317	0.211	0.238	0.206
04	-3.451	-1.826	-4.687	1.334
05	1.367	-4.211	-2.915	-4.687
06	1.379	-4.687	-4.687	-4.687
07	-4.687	-4.687	-4.687	1.379
08	-4.687	-4.687	-4.687	1.379
09	1.379	-4.687	-4.687	-4.687
10	1.033	-1.862	0.015	-3.889
11	-0.842	-0.457	-0.791	0.909
12	-0.997	0.053	-0.147	0.538
13	-0.153	0.281	-0.286	0.064
14	0.188	-0.059	-0.348	0.135

Standard thresholds

P-value	Threshold
0.001	2.86076
0.0005	4.01416
0.0001	7.19062