LHX8.H12RSNP.1.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX8.H12RSNP.1.M.C
Gene (human)	LHX8 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lhx8
Gene synonyms (mouse)	Lhx7
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	C

Motif length	13
Consensus	nvCTMGTTARbbn
GC content	43.82%
Information content (bits; total / per base)	12.329 / 0.948
Data sources	Methyl-HT-SELEX
Aligned words	2034

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.933	0.887	0.917	0.869	0.87	0.829
Overall, 4 experiments	best	0.986	0.977	0.975	0.962	0.949	0.931
Methyl HT-SELEX, 1 experiments	median	0.986	0.977	0.975	0.962	0.949	0.931
Methyl HT-SELEX, 1 experiments	best	0.986	0.977	0.975	0.962	0.949	0.931
Non-Methyl HT-SELEX, 3 experiments	median	0.906	0.848	0.888	0.829	0.817	0.774
Non-Methyl HT-SELEX, 3 experiments	best	0.959	0.926	0.945	0.91	0.923	0.884

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.744	0.072	0.664	0.399
batch 2	0.579	0.233	0.34	0.288

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.H12RSNP.1.M.C.pcm
PWM	LHX8.H12RSNP.1.M.C.pwm
PFM	LHX8.H12RSNP.1.M.C.pfm
Alignment	LHX8.H12RSNP.1.M.C.words.tsv
Threshold to P-value map	LHX8.H12RSNP.1.M.C.thr
Motif in other formats
JASPAR format	LHX8.H12RSNP.1.M.C_jaspar_format.txt
MEME format	LHX8.H12RSNP.1.M.C_meme_format.meme
Transfac format	LHX8.H12RSNP.1.M.C_transfac_format.txt
Homer format	LHX8.H12RSNP.1.M.C_homer_format_0.001.txt LHX8.H12RSNP.1.M.C_homer_format_0.0005.txt LHX8.H12RSNP.1.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	601.25	492.25	423.25	517.25
02	323.25	715.25	823.25	172.25
03	204.0	1636.0	160.0	34.0
04	0.0	11.0	0.0	2023.0
05	492.0	1469.0	73.0	0.0
06	608.0	0.0	1426.0	0.0
07	0.0	0.0	0.0	2034.0
08	0.0	1.0	0.0	2033.0
09	2022.0	0.0	10.0	2.0
10	1012.0	139.0	826.0	57.0
11	56.0	838.0	361.0	779.0
12	205.75	493.75	747.75	586.75
13	681.5	463.5	477.5	411.5

PFM

	A	C	G	T
01	0.296	0.242	0.208	0.254
02	0.159	0.352	0.405	0.085
03	0.1	0.804	0.079	0.017
04	0.0	0.005	0.0	0.995
05	0.242	0.722	0.036	0.0
06	0.299	0.0	0.701	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	0.994	0.0	0.005	0.001
10	0.498	0.068	0.406	0.028
11	0.028	0.412	0.177	0.383
12	0.101	0.243	0.368	0.288
13	0.335	0.228	0.235	0.202

PWM

	A	C	G	T
01	0.167	-0.032	-0.183	0.017
02	-0.451	0.34	0.48	-1.075
03	-0.908	1.166	-1.148	-2.654
04	-5.591	-3.678	-5.591	1.378
05	-0.033	1.058	-1.919	-5.591
06	0.178	-5.591	1.029	-5.591
07	-5.591	-5.591	-5.591	1.383
08	-5.591	-5.169	-5.591	1.383
09	1.378	-5.591	-3.758	-4.873
10	0.686	-1.287	0.484	-2.159
11	-2.176	0.498	-0.341	0.425
12	-0.899	-0.029	0.384	0.143
13	0.292	-0.092	-0.063	-0.211

Standard thresholds

P-value	Threshold
0.001	3.27311
0.0005	4.84961
0.0001	7.53312