LHX8.H12INVIVO.0.S.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX8.H12INVIVO.0.S.D
Gene (human)	LHX8 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lhx8
Gene synonyms (mouse)	Lhx7
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	13
Consensus	nvRYTAATTASnn
GC content	34.95%
Information content (bits; total / per base)	12.834 / 0.987
Data sources	HT-SELEX
Aligned words	7700

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.981	0.969	0.971	0.955	0.924	0.908
Overall, 4 experiments	best	0.986	0.977	0.98	0.967	0.971	0.954
Methyl HT-SELEX, 1 experiments	median	0.978	0.962	0.968	0.948	0.938	0.914
Methyl HT-SELEX, 1 experiments	best	0.978	0.962	0.968	0.948	0.938	0.914
Non-Methyl HT-SELEX, 3 experiments	median	0.985	0.976	0.975	0.962	0.91	0.901
Non-Methyl HT-SELEX, 3 experiments	best	0.986	0.977	0.98	0.967	0.971	0.954

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.976	0.726	0.947	0.605
batch 2	0.655	0.503	0.59	0.611

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.0.S.D.pcm
PWM	LHX8.H12INVIVO.0.S.D.pwm
PFM	LHX8.H12INVIVO.0.S.D.pfm
Alignment	LHX8.H12INVIVO.0.S.D.words.tsv
Threshold to P-value map	LHX8.H12INVIVO.0.S.D.thr
Motif in other formats
JASPAR format	LHX8.H12INVIVO.0.S.D_jaspar_format.txt
MEME format	LHX8.H12INVIVO.0.S.D_meme_format.meme
Transfac format	LHX8.H12INVIVO.0.S.D_transfac_format.txt
Homer format	LHX8.H12INVIVO.0.S.D_homer_format_0.001.txt LHX8.H12INVIVO.0.S.D_homer_format_0.0005.txt LHX8.H12INVIVO.0.S.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1593.25	1581.25	1908.25	2617.25
02	1904.5	2734.5	2141.5	919.5
03	3295.0	1416.0	2926.0	63.0
04	24.0	4290.0	279.0	3107.0
05	0.0	0.0	0.0	7700.0
06	6766.0	0.0	934.0	0.0
07	7700.0	0.0	0.0	0.0
08	0.0	0.0	0.0	7700.0
09	0.0	0.0	0.0	7700.0
10	6491.0	1.0	1207.0	1.0
11	400.0	3595.0	3410.0	295.0
12	1353.5	2735.5	2146.5	1464.5
13	2082.5	2073.5	1608.5	1935.5

PFM

	A	C	G	T
01	0.207	0.205	0.248	0.34
02	0.247	0.355	0.278	0.119
03	0.428	0.184	0.38	0.008
04	0.003	0.557	0.036	0.404
05	0.0	0.0	0.0	1.0
06	0.879	0.0	0.121	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	0.843	0.0	0.157	0.0
11	0.052	0.467	0.443	0.038
12	0.176	0.355	0.279	0.19
13	0.27	0.269	0.209	0.251

PWM

	A	C	G	T
01	-0.189	-0.196	-0.009	0.307
02	-0.011	0.351	0.106	-0.738
03	0.537	-0.307	0.418	-3.386
04	-4.297	0.801	-1.925	0.478
05	-6.759	-6.759	-6.759	1.385
06	1.256	-6.759	-0.722	-6.759
07	1.385	-6.759	-6.759	-6.759
08	-6.759	-6.759	-6.759	1.385
09	-6.759	-6.759	-6.759	1.385
10	1.215	-6.389	-0.466	-6.389
11	-1.567	0.624	0.571	-1.869
12	-0.352	0.351	0.109	-0.273
13	0.079	0.074	-0.179	0.005

Standard thresholds

P-value	Threshold
0.001	1.51741
0.0005	3.58151
0.0001	7.595665