LHX5.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX5.H12RSNP.0.PSM.A
Gene (human)	LHX5 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lhx5
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	nnvYTAATTAbn
GC content	30.71%
Information content (bits; total / per base)	11.878 / 0.99
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9144

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.965	0.941	0.948	0.919	0.893	0.865
Overall, 2 experiments	best	0.972	0.951	0.959	0.934	0.914	0.888
Methyl HT-SELEX, 1 experiments	median	0.959	0.932	0.936	0.903	0.872	0.842
Methyl HT-SELEX, 1 experiments	best	0.959	0.932	0.936	0.903	0.872	0.842
Non-Methyl HT-SELEX, 1 experiments	median	0.972	0.951	0.959	0.934	0.914	0.888
Non-Methyl HT-SELEX, 1 experiments	best	0.972	0.951	0.959	0.934	0.914	0.888

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.987	0.741	0.932	0.427
batch 2	0.61	0.277	0.559	0.334

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	LHX1-like {3.1.5.2} (TFClass)
TFClass ID	TFClass: 3.1.5.2.2
HGNC	HGNC:14216
MGI	MGI:107792
EntrezGene (human)	GeneID:64211 (SSTAR profile)
EntrezGene (mouse)	GeneID:16873 (SSTAR profile)
UniProt ID (human)	LHX5_HUMAN
UniProt ID (mouse)	LHX5_MOUSE
UniProt AC (human)	Q9H2C1 (TFClass)
UniProt AC (mouse)	P61375 (TFClass)
GRECO-DB-TF	yes

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

PCM	LHX5.H12RSNP.0.PSM.A.pcm
PWM	LHX5.H12RSNP.0.PSM.A.pwm
PFM	LHX5.H12RSNP.0.PSM.A.pfm
Alignment	LHX5.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	LHX5.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	LHX5.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	LHX5.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	LHX5.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	LHX5.H12RSNP.0.PSM.A_homer_format_0.001.txt LHX5.H12RSNP.0.PSM.A_homer_format_0.0005.txt LHX5.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2167.5	2163.5	2451.5	2361.5
02	2729.75	2943.75	2193.75	1276.75
03	3234.0	2088.0	3411.0	411.0
04	195.0	2858.0	1537.0	4554.0
05	0.0	0.0	0.0	9144.0
06	9144.0	0.0	0.0	0.0
07	9144.0	0.0	0.0	0.0
08	0.0	0.0	0.0	9144.0
09	0.0	10.0	17.0	9117.0
10	6273.0	28.0	2780.0	63.0
11	1330.25	3763.25	2678.25	1372.25
12	2112.5	2389.5	2383.5	2258.5

PFM

	A	C	G	T
01	0.237	0.237	0.268	0.258
02	0.299	0.322	0.24	0.14
03	0.354	0.228	0.373	0.045
04	0.021	0.313	0.168	0.498
05	0.0	0.0	0.0	1.0
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.001	0.002	0.997
10	0.686	0.003	0.304	0.007
11	0.145	0.412	0.293	0.15
12	0.231	0.261	0.261	0.247

PWM

	A	C	G	T
01	-0.053	-0.055	0.07	0.032
02	0.177	0.253	-0.041	-0.582
03	0.347	-0.091	0.4	-1.711
04	-2.451	0.223	-0.396	0.689
05	-6.911	-6.911	-6.911	1.386
06	1.386	-6.911	-6.911	-6.911
07	1.386	-6.911	-6.911	-6.911
08	-6.911	-6.911	-6.911	1.386
09	-6.911	-5.228	-4.776	1.383
10	1.009	-4.325	0.195	-3.557
11	-0.541	0.498	0.158	-0.51
12	-0.079	0.044	0.042	-0.012

Standard thresholds

P-value	Threshold
0.001	1.68207
0.0005	4.044395
0.0001	8.08798