LHX8.H12INVIVO.1.M.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX8.H12INVIVO.1.M.D
Gene (human)	LHX8 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lhx8
Gene synonyms (mouse)	Lhx7
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	13
Consensus	nvCTMGTTARYbn
GC content	42.7%
Information content (bits; total / per base)	12.222 / 0.94
Data sources	Methyl-HT-SELEX
Aligned words	1951

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.941	0.9	0.925	0.881	0.877	0.839
Overall, 4 experiments	best	0.985	0.975	0.974	0.959	0.948	0.928
Methyl HT-SELEX, 1 experiments	median	0.985	0.975	0.974	0.959	0.948	0.928
Methyl HT-SELEX, 1 experiments	best	0.985	0.975	0.974	0.959	0.948	0.928
Non-Methyl HT-SELEX, 3 experiments	median	0.919	0.864	0.899	0.844	0.827	0.786
Non-Methyl HT-SELEX, 3 experiments	best	0.964	0.936	0.95	0.919	0.927	0.892

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.784	0.092	0.735	0.43
batch 2	0.57	0.222	0.321	0.258

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	LHX6-like {3.1.5.5} (TFClass)
TFClass ID	TFClass: 3.1.5.5.2
HGNC	HGNC:28838
MGI	MGI:1096343
EntrezGene (human)	GeneID:431707 (SSTAR profile)
EntrezGene (mouse)	GeneID:16875 (SSTAR profile)
UniProt ID (human)	LHX8_HUMAN
UniProt ID (mouse)	LHX8_MOUSE
UniProt AC (human)	Q68G74 (TFClass)
UniProt AC (mouse)	O35652 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	LHX8.H12INVIVO.1.M.D.pcm
PWM	LHX8.H12INVIVO.1.M.D.pwm
PFM	LHX8.H12INVIVO.1.M.D.pfm
Alignment	LHX8.H12INVIVO.1.M.D.words.tsv
Threshold to P-value map	LHX8.H12INVIVO.1.M.D.thr
Motif in other formats
JASPAR format	LHX8.H12INVIVO.1.M.D_jaspar_format.txt
MEME format	LHX8.H12INVIVO.1.M.D_meme_format.meme
Transfac format	LHX8.H12INVIVO.1.M.D_transfac_format.txt
Homer format	LHX8.H12INVIVO.1.M.D_homer_format_0.001.txt LHX8.H12INVIVO.1.M.D_homer_format_0.0005.txt LHX8.H12INVIVO.1.M.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	520.75	487.75	454.75	487.75
02	378.5	612.5	768.5	191.5
03	161.0	1606.0	146.0	38.0
04	0.0	1.0	1.0	1949.0
05	556.0	1296.0	99.0	0.0
06	696.0	0.0	1255.0	0.0
07	0.0	0.0	0.0	1951.0
08	0.0	0.0	0.0	1951.0
09	1936.0	0.0	15.0	0.0
10	970.0	156.0	775.0	50.0
11	36.0	844.0	300.0	771.0
12	221.0	412.0	745.0	573.0
13	682.5	424.5	430.5	413.5

PFM

	A	C	G	T
01	0.267	0.25	0.233	0.25
02	0.194	0.314	0.394	0.098
03	0.083	0.823	0.075	0.019
04	0.0	0.001	0.001	0.999
05	0.285	0.664	0.051	0.0
06	0.357	0.0	0.643	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	0.992	0.0	0.008	0.0
10	0.497	0.08	0.397	0.026
11	0.018	0.433	0.154	0.395
12	0.113	0.211	0.382	0.294
13	0.35	0.218	0.221	0.212

PWM

	A	C	G	T
01	0.065	0.0	-0.07	0.0
02	-0.252	0.227	0.453	-0.929
03	-1.101	1.189	-1.197	-2.507
04	-5.555	-5.131	-5.131	1.382
05	0.13	0.975	-1.58	-5.555
06	0.354	-5.555	0.943	-5.555
07	-5.555	-5.555	-5.555	1.383
08	-5.555	-5.555	-5.555	1.383
09	1.376	-5.555	-3.367	-5.555
10	0.686	-1.132	0.462	-2.244
11	-2.559	0.547	-0.484	0.456
12	-0.787	-0.168	0.422	0.161
13	0.335	-0.138	-0.124	-0.164

Standard thresholds

P-value	Threshold
0.001	3.258575
0.0005	4.945915
0.0001	7.56071