LHX8.H12INVITRO.1.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX8.H12INVITRO.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	nvSTMGTTARbbn
GC content	44.13%
Information content (bits; total / per base)	12.229 / 0.941
Data sources	Methyl-HT-SELEX
Aligned words	6215

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.945	0.905	0.927	0.886	0.879	0.843
Overall, 4 experiments	best	0.986	0.977	0.975	0.961	0.95	0.931
Methyl HT-SELEX, 1 experiments	median	0.986	0.977	0.975	0.961	0.95	0.931
Methyl HT-SELEX, 1 experiments	best	0.986	0.977	0.975	0.961	0.95	0.931
Non-Methyl HT-SELEX, 3 experiments	median	0.923	0.869	0.901	0.848	0.83	0.789
Non-Methyl HT-SELEX, 3 experiments	best	0.967	0.942	0.954	0.925	0.929	0.896

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.682	0.079	0.612	0.363
batch 2	0.519	0.224	0.348	0.298

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.1.M.C.pcm
PWM	LHX8.H12INVITRO.1.M.C.pwm
PFM	LHX8.H12INVITRO.1.M.C.pfm
Alignment	LHX8.H12INVITRO.1.M.C.words.tsv
Threshold to P-value map	LHX8.H12INVITRO.1.M.C.thr
Motif in other formats
JASPAR format	LHX8.H12INVITRO.1.M.C_jaspar_format.txt
MEME format	LHX8.H12INVITRO.1.M.C_meme_format.meme
Transfac format	LHX8.H12INVITRO.1.M.C_transfac_format.txt
Homer format	LHX8.H12INVITRO.1.M.C_homer_format_0.001.txt LHX8.H12INVITRO.1.M.C_homer_format_0.0005.txt LHX8.H12INVITRO.1.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1829.75	1498.75	1441.75	1444.75
02	988.0	2165.0	2446.0	616.0
03	468.0	4790.0	907.0	50.0
04	0.0	40.0	0.0	6175.0
05	1917.0	4114.0	184.0	0.0
06	2286.0	0.0	3929.0	0.0
07	0.0	0.0	0.0	6215.0
08	0.0	2.0	0.0	6213.0
09	6215.0	0.0	0.0	0.0
10	2796.0	359.0	2889.0	171.0
11	140.0	2933.0	1002.0	2140.0
12	808.25	1293.25	2672.25	1441.25
13	1860.75	1483.75	1502.75	1367.75

PFM

	A	C	G	T
01	0.294	0.241	0.232	0.232
02	0.159	0.348	0.394	0.099
03	0.075	0.771	0.146	0.008
04	0.0	0.006	0.0	0.994
05	0.308	0.662	0.03	0.0
06	0.368	0.0	0.632	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	1.0	0.0	0.0	0.0
10	0.45	0.058	0.465	0.028
11	0.023	0.472	0.161	0.344
12	0.13	0.208	0.43	0.232
13	0.299	0.239	0.242	0.22

PWM

	A	C	G	T
01	0.163	-0.036	-0.075	-0.073
02	-0.452	0.331	0.453	-0.923
03	-1.197	1.125	-0.537	-3.395
04	-6.569	-3.608	-6.569	1.379
05	0.21	0.973	-2.123	-6.569
06	0.386	-6.569	0.927	-6.569
07	-6.569	-6.569	-6.569	1.385
08	-6.569	-5.919	-6.569	1.385
09	1.385	-6.569	-6.569	-6.569
10	0.587	-1.46	0.62	-2.195
11	-2.393	0.635	-0.438	0.32
12	-0.652	-0.183	0.542	-0.075
13	0.18	-0.046	-0.033	-0.127

Standard thresholds

P-value	Threshold
0.001	2.80957
0.0005	4.81861
0.0001	7.651275