LHX6.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX6.H12INVIVO.0.P.B
Gene (human)	LHX6 (GeneCards)
Gene synonyms (human)	LHX6.1
Gene (mouse)	Lhx6
Gene synonyms (mouse)	Lhx6.1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	10
Consensus	bYAATCARnn
GC content	40.07%
Information content (bits; total / per base)	10.345 / 1.034
Data sources	ChIP-Seq
Aligned words	888

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Mouse	2 (12)	0.875	0.927	0.805	0.845	0.804	0.842	2.418	2.52	170.933	203.495

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.81	0.786	0.77	0.756	0.747	0.736
Overall, 4 experiments	best	0.985	0.974	0.978	0.963	0.968	0.95
Methyl HT-SELEX, 1 experiments	median	0.978	0.964	0.97	0.951	0.959	0.935
Methyl HT-SELEX, 1 experiments	best	0.978	0.964	0.97	0.951	0.959	0.935
Non-Methyl HT-SELEX, 3 experiments	median	0.641	0.608	0.569	0.562	0.535	0.538
Non-Methyl HT-SELEX, 3 experiments	best	0.985	0.974	0.978	0.963	0.968	0.95

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.91	0.741	0.907	0.598

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: 3.1.5.5.1
HGNC	HGNC:21735
MGI	MGI:1306803
EntrezGene (human)	GeneID:26468 (SSTAR profile)
EntrezGene (mouse)	GeneID:16874 (SSTAR profile)
UniProt ID (human)	LHX6_HUMAN
UniProt ID (mouse)	LHX6_MOUSE
UniProt AC (human)	Q9UPM6 (TFClass)
UniProt AC (mouse)	Q9R1R0 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 2 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	LHX6.H12INVIVO.0.P.B.pcm
PWM	LHX6.H12INVIVO.0.P.B.pwm
PFM	LHX6.H12INVIVO.0.P.B.pfm
Alignment	LHX6.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	LHX6.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	LHX6.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	LHX6.H12INVIVO.0.P.B_meme_format.meme
Transfac format	LHX6.H12INVIVO.0.P.B_transfac_format.txt
Homer format	LHX6.H12INVIVO.0.P.B_homer_format_0.001.txt LHX6.H12INVIVO.0.P.B_homer_format_0.0005.txt LHX6.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	65.0	274.0	405.0	144.0
02	33.0	391.0	8.0	456.0
03	822.0	64.0	1.0	1.0
04	878.0	3.0	2.0	5.0
05	0.0	1.0	1.0	886.0
06	0.0	792.0	18.0	78.0
07	881.0	1.0	0.0	6.0
08	223.0	103.0	503.0	59.0
09	282.0	227.0	238.0	141.0
10	232.0	233.0	293.0	130.0

PFM

	A	C	G	T
01	0.073	0.309	0.456	0.162
02	0.037	0.44	0.009	0.514
03	0.926	0.072	0.001	0.001
04	0.989	0.003	0.002	0.006
05	0.0	0.001	0.001	0.998
06	0.0	0.892	0.02	0.088
07	0.992	0.001	0.0	0.007
08	0.251	0.116	0.566	0.066
09	0.318	0.256	0.268	0.159
10	0.261	0.262	0.33	0.146

PWM

	A	C	G	T
01	-1.21	0.209	0.598	-0.429
02	-1.864	0.563	-3.138	0.716
03	1.304	-1.225	-4.418	-4.418
04	1.369	-3.863	-4.103	-3.509
05	-4.881	-4.418	-4.418	1.378
06	-4.881	1.266	-2.43	-1.032
07	1.373	-4.418	-4.881	-3.369
08	0.004	-0.759	0.814	-1.304
09	0.238	0.022	0.069	-0.45
10	0.044	0.048	0.276	-0.53

Standard thresholds

P-value	Threshold
0.001	4.66891
0.0005	5.81938
0.0001	7.752165