LHX4.H12INVITRO.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX4.H12INVITRO.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	12
Consensus	nbTAATTARbnn
GC content	31.1%
Information content (bits; total / per base)	11.763 / 0.98
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8585

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.946	0.912	0.912	0.875	0.828	0.8
Overall, 6 experiments	best	0.979	0.968	0.956	0.938	0.851	0.846
Methyl HT-SELEX, 2 experiments	median	0.962	0.94	0.93	0.901	0.841	0.82
Methyl HT-SELEX, 2 experiments	best	0.962	0.941	0.931	0.901	0.845	0.823
Non-Methyl HT-SELEX, 4 experiments	median	0.803	0.771	0.737	0.716	0.677	0.665
Non-Methyl HT-SELEX, 4 experiments	best	0.979	0.968	0.956	0.938	0.851	0.846

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.79	0.603	0.822	0.619

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.H12INVITRO.0.SM.B.pcm
PWM	LHX4.H12INVITRO.0.SM.B.pwm
PFM	LHX4.H12INVITRO.0.SM.B.pfm
Alignment	LHX4.H12INVITRO.0.SM.B.words.tsv
Threshold to P-value map	LHX4.H12INVITRO.0.SM.B.thr
Motif in other formats
JASPAR format	LHX4.H12INVITRO.0.SM.B_jaspar_format.txt
MEME format	LHX4.H12INVITRO.0.SM.B_meme_format.meme
Transfac format	LHX4.H12INVITRO.0.SM.B_transfac_format.txt
Homer format	LHX4.H12INVITRO.0.SM.B_homer_format_0.001.txt LHX4.H12INVITRO.0.SM.B_homer_format_0.0005.txt LHX4.H12INVITRO.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1975.75	2420.75	2137.75	2050.75
02	942.0	2775.0	3435.0	1433.0
03	119.0	2267.0	68.0	6131.0
04	7957.0	42.0	583.0	3.0
05	8585.0	0.0	0.0	0.0
06	0.0	0.0	0.0	8585.0
07	0.0	0.0	0.0	8585.0
08	8585.0	0.0	0.0	0.0
09	4426.0	954.0	3186.0	19.0
10	313.0	3407.0	1653.0	3212.0
11	1394.0	1948.0	3239.0	2004.0
12	2694.5	2022.5	1900.5	1967.5

PFM

	A	C	G	T
01	0.23	0.282	0.249	0.239
02	0.11	0.323	0.4	0.167
03	0.014	0.264	0.008	0.714
04	0.927	0.005	0.068	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	0.111	0.371	0.002
10	0.036	0.397	0.193	0.374
11	0.162	0.227	0.377	0.233
12	0.314	0.236	0.221	0.229

PWM

	A	C	G	T
01	-0.083	0.12	-0.004	-0.045
02	-0.822	0.257	0.47	-0.403
03	-2.875	0.055	-3.42	1.049
04	1.31	-3.882	-1.3	-6.012
05	1.386	-6.855	-6.855	-6.855
06	-6.855	-6.855	-6.855	1.386
07	-6.855	-6.855	-6.855	1.386
08	1.386	-6.855	-6.855	-6.855
09	0.723	-0.809	0.395	-4.615
10	-1.919	0.462	-0.261	0.403
11	-0.431	-0.097	0.411	-0.069
12	0.227	-0.059	-0.121	-0.087

Standard thresholds

P-value	Threshold
0.001	3.060915
0.0005	4.996735
0.0001	7.962015