LHX5.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX5.H12INVITRO.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	nvvYTAATTAvn
GC content	31.49%
Information content (bits; total / per base)	11.599 / 0.967
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	8209

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.965	0.942	0.948	0.919	0.899	0.87
Overall, 2 experiments	best	0.971	0.95	0.96	0.934	0.917	0.891
Methyl HT-SELEX, 1 experiments	median	0.959	0.933	0.937	0.905	0.88	0.849
Methyl HT-SELEX, 1 experiments	best	0.959	0.933	0.937	0.905	0.88	0.849
Non-Methyl HT-SELEX, 1 experiments	median	0.971	0.95	0.96	0.934	0.917	0.891
Non-Methyl HT-SELEX, 1 experiments	best	0.971	0.95	0.96	0.934	0.917	0.891

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.98	0.699	0.914	0.427
batch 2	0.596	0.252	0.537	0.332

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.H12INVITRO.0.PSM.A.pcm
PWM	LHX5.H12INVITRO.0.PSM.A.pwm
PFM	LHX5.H12INVITRO.0.PSM.A.pfm
Alignment	LHX5.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	LHX5.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	LHX5.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	LHX5.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	LHX5.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	LHX5.H12INVITRO.0.PSM.A_homer_format_0.001.txt LHX5.H12INVITRO.0.PSM.A_homer_format_0.0005.txt LHX5.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1958.75	2015.75	1931.75	2302.75
02	1878.75	3618.75	1397.75	1313.75
03	2355.0	1513.0	4042.0	299.0
04	479.0	1930.0	1031.0	4769.0
05	0.0	1.0	0.0	8208.0
06	8209.0	0.0	0.0	0.0
07	8209.0	0.0	0.0	0.0
08	0.0	154.0	0.0	8055.0
09	3.0	87.0	489.0	7630.0
10	5575.0	17.0	2570.0	47.0
11	1267.0	2694.0	3271.0	977.0
12	1897.25	1669.25	2590.25	2052.25

PFM

	A	C	G	T
01	0.239	0.246	0.235	0.281
02	0.229	0.441	0.17	0.16
03	0.287	0.184	0.492	0.036
04	0.058	0.235	0.126	0.581
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	0.019	0.0	0.981
09	0.0	0.011	0.06	0.929
10	0.679	0.002	0.313	0.006
11	0.154	0.328	0.398	0.119
12	0.231	0.203	0.316	0.25

PWM

	A	C	G	T
01	-0.047	-0.018	-0.06	0.115
02	-0.088	0.567	-0.384	-0.445
03	0.137	-0.304	0.677	-1.92
04	-1.451	-0.061	-0.687	0.843
05	-6.815	-6.448	-6.815	1.385
06	1.385	-6.815	-6.815	-6.815
07	1.385	-6.815	-6.815	-6.815
08	-6.815	-2.576	-6.815	1.367
09	-5.969	-3.136	-1.431	1.312
10	0.999	-4.67	0.225	-3.731
11	-0.482	0.272	0.466	-0.741
12	-0.078	-0.206	0.233	0.0

Standard thresholds

P-value	Threshold
0.001	3.632915
0.0005	5.217635
0.0001	7.81802