LHX8.H12INVITRO.0.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX8.H12INVITRO.0.S.B
Gene (human)	LHX8 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lhx8
Gene synonyms (mouse)	Lhx7
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	12
Consensus	nnvYTAATTASn
GC content	34.95%
Information content (bits; total / per base)	12.335 / 1.028
Data sources	HT-SELEX
Aligned words	7448

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.983	0.971	0.973	0.957	0.922	0.908
Overall, 4 experiments	best	0.988	0.981	0.978	0.966	0.971	0.954
Methyl HT-SELEX, 1 experiments	median	0.978	0.964	0.968	0.949	0.935	0.912
Methyl HT-SELEX, 1 experiments	best	0.978	0.964	0.968	0.949	0.935	0.912
Non-Methyl HT-SELEX, 3 experiments	median	0.987	0.978	0.978	0.965	0.91	0.903
Non-Methyl HT-SELEX, 3 experiments	best	0.988	0.981	0.978	0.966	0.971	0.954

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.97	0.666	0.952	0.597
batch 2	0.649	0.45	0.606	0.62

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.H12INVITRO.0.S.B.pcm
PWM	LHX8.H12INVITRO.0.S.B.pwm
PFM	LHX8.H12INVITRO.0.S.B.pfm
Alignment	LHX8.H12INVITRO.0.S.B.words.tsv
Threshold to P-value map	LHX8.H12INVITRO.0.S.B.thr
Motif in other formats
JASPAR format	LHX8.H12INVITRO.0.S.B_jaspar_format.txt
MEME format	LHX8.H12INVITRO.0.S.B_meme_format.meme
Transfac format	LHX8.H12INVITRO.0.S.B_transfac_format.txt
Homer format	LHX8.H12INVITRO.0.S.B_homer_format_0.001.txt LHX8.H12INVITRO.0.S.B_homer_format_0.0005.txt LHX8.H12INVITRO.0.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1689.25	1493.25	1827.25	2438.25
02	1710.75	2578.75	1834.75	1323.75
03	2612.0	1268.0	3390.0	178.0
04	0.0	4208.0	23.0	3217.0
05	0.0	0.0	0.0	7448.0
06	5085.0	0.0	2363.0	0.0
07	7448.0	0.0	0.0	0.0
08	0.0	0.0	0.0	7448.0
09	0.0	0.0	0.0	7448.0
10	5609.0	0.0	1839.0	0.0
11	437.0	3726.0	3087.0	198.0
12	1952.75	2022.75	1575.75	1896.75

PFM

	A	C	G	T
01	0.227	0.2	0.245	0.327
02	0.23	0.346	0.246	0.178
03	0.351	0.17	0.455	0.024
04	0.0	0.565	0.003	0.432
05	0.0	0.0	0.0	1.0
06	0.683	0.0	0.317	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.0	0.0	1.0
10	0.753	0.0	0.247	0.0
11	0.059	0.5	0.414	0.027
12	0.262	0.272	0.212	0.255

PWM

	A	C	G	T
01	-0.097	-0.22	-0.019	0.269
02	-0.085	0.325	-0.015	-0.341
03	0.338	-0.384	0.599	-2.336
04	-6.729	0.815	-4.303	0.546
05	-6.729	-6.729	-6.729	1.385
06	1.004	-6.729	0.238	-6.729
07	1.385	-6.729	-6.729	-6.729
08	-6.729	-6.729	-6.729	1.385
09	-6.729	-6.729	-6.729	1.385
10	1.102	-6.729	-0.012	-6.729
11	-1.446	0.693	0.505	-2.231
12	0.048	0.083	-0.167	0.018

Standard thresholds

P-value	Threshold
0.001	1.15416
0.0005	3.18843
0.0001	8.028905