LHX6.H12CORE.2.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX6.H12CORE.2.M.C
Gene (human)	LHX6 (GeneCards)
Gene synonyms (human)	LHX6.1
Gene (mouse)	Lhx6
Gene synonyms (mouse)	Lhx6.1
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	C

Motif length	13
Consensus	nvvYTAACKAGbn
GC content	44.61%
Information content (bits; total / per base)	12.468 / 0.959
Data sources	Methyl-HT-SELEX
Aligned words	1987

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)	0.716	0.802	0.513	0.662	0.595	0.748	1.352	2.04	31.216	55.824

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.792	0.767	0.759	0.742	0.733	0.719
Overall, 4 experiments	best	0.991	0.986	0.983	0.974	0.97	0.956
Methyl HT-SELEX, 1 experiments	median	0.991	0.986	0.983	0.974	0.97	0.956
Methyl HT-SELEX, 1 experiments	best	0.991	0.986	0.983	0.974	0.97	0.956
Non-Methyl HT-SELEX, 3 experiments	median	0.612	0.583	0.558	0.549	0.529	0.53
Non-Methyl HT-SELEX, 3 experiments	best	0.972	0.95	0.961	0.935	0.938	0.909

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.746	0.249	0.649	0.359

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.H12CORE.2.M.C.pcm
PWM	LHX6.H12CORE.2.M.C.pwm
PFM	LHX6.H12CORE.2.M.C.pfm
Alignment	LHX6.H12CORE.2.M.C.words.tsv
Threshold to P-value map	LHX6.H12CORE.2.M.C.thr
Motif in other formats
JASPAR format	LHX6.H12CORE.2.M.C_jaspar_format.txt
MEME format	LHX6.H12CORE.2.M.C_meme_format.meme
Transfac format	LHX6.H12CORE.2.M.C_transfac_format.txt
Homer format	LHX6.H12CORE.2.M.C_homer_format_0.001.txt LHX6.H12CORE.2.M.C_homer_format_0.0005.txt LHX6.H12CORE.2.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	470.5	445.5	450.5	620.5
02	500.25	812.25	469.25	205.25
03	669.0	412.0	858.0	48.0
04	25.0	945.0	96.0	921.0
05	0.0	7.0	0.0	1980.0
06	1987.0	0.0	0.0	0.0
07	1987.0	0.0	0.0	0.0
08	0.0	1231.0	0.0	756.0
09	0.0	146.0	1270.0	571.0
10	1982.0	0.0	5.0	0.0
11	25.0	156.0	1705.0	101.0
12	123.5	854.5	688.5	320.5
13	448.5	511.5	460.5	566.5

PFM

	A	C	G	T
01	0.237	0.224	0.227	0.312
02	0.252	0.409	0.236	0.103
03	0.337	0.207	0.432	0.024
04	0.013	0.476	0.048	0.464
05	0.0	0.004	0.0	0.996
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.62	0.0	0.38
09	0.0	0.073	0.639	0.287
10	0.997	0.0	0.003	0.0
11	0.013	0.079	0.858	0.051
12	0.062	0.43	0.347	0.161
13	0.226	0.257	0.232	0.285

PWM

	A	C	G	T
01	-0.054	-0.108	-0.097	0.222
02	0.007	0.49	-0.057	-0.878
03	0.297	-0.186	0.545	-2.302
04	-2.92	0.641	-1.628	0.616
05	-5.571	-4.026	-5.571	1.38
06	1.383	-5.571	-5.571	-5.571
07	1.383	-5.571	-5.571	-5.571
08	-5.571	0.905	-5.571	0.419
09	-5.571	-1.215	0.936	0.139
10	1.381	-5.571	-4.281	-5.571
11	-2.92	-1.15	1.231	-1.578
12	-1.38	0.541	0.325	-0.436
13	-0.102	0.029	-0.075	0.131

Standard thresholds

P-value	Threshold
0.001	3.05236
0.0005	4.672115
0.0001	7.518375