LHX6.H12INVIVO.2.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX6.H12INVIVO.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	46.93%
Information content (bits; total / per base)	12.62 / 0.971
Data sources	Methyl-HT-SELEX
Aligned words	6706

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)	0.704	0.802	0.506	0.663	0.601	0.754	1.371	2.019	29.828	50.854

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.788	0.762	0.756	0.738	0.73	0.715
Overall, 4 experiments	best	0.993	0.988	0.985	0.977	0.972	0.959
Methyl HT-SELEX, 1 experiments	median	0.993	0.988	0.985	0.977	0.972	0.959
Methyl HT-SELEX, 1 experiments	best	0.993	0.988	0.985	0.977	0.972	0.959
Non-Methyl HT-SELEX, 3 experiments	median	0.606	0.577	0.553	0.546	0.526	0.527
Non-Methyl HT-SELEX, 3 experiments	best	0.969	0.946	0.958	0.931	0.934	0.904

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.751	0.237	0.633	0.34

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.2.M.C.pcm
PWM	LHX6.H12INVIVO.2.M.C.pwm
PFM	LHX6.H12INVIVO.2.M.C.pfm
Alignment	LHX6.H12INVIVO.2.M.C.words.tsv
Threshold to P-value map	LHX6.H12INVIVO.2.M.C.thr
Motif in other formats
JASPAR format	LHX6.H12INVIVO.2.M.C_jaspar_format.txt
MEME format	LHX6.H12INVIVO.2.M.C_meme_format.meme
Transfac format	LHX6.H12INVIVO.2.M.C_transfac_format.txt
Homer format	LHX6.H12INVIVO.2.M.C_homer_format_0.001.txt LHX6.H12INVIVO.2.M.C_homer_format_0.0005.txt LHX6.H12INVIVO.2.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1543.25	1583.25	1736.25	1843.25
02	1428.5	2987.5	1457.5	832.5
03	2028.0	1476.0	3011.0	191.0
04	171.0	3877.0	365.0	2293.0
05	1.0	3.0	0.0	6702.0
06	6706.0	0.0	0.0	0.0
07	6706.0	0.0	0.0	0.0
08	0.0	4539.0	0.0	2167.0
09	0.0	406.0	4713.0	1587.0
10	6703.0	0.0	3.0	0.0
11	74.0	636.0	5683.0	313.0
12	514.75	3038.75	2284.75	867.75
13	1603.0	1718.0	1397.0	1988.0

PFM

	A	C	G	T
01	0.23	0.236	0.259	0.275
02	0.213	0.445	0.217	0.124
03	0.302	0.22	0.449	0.028
04	0.025	0.578	0.054	0.342
05	0.0	0.0	0.0	0.999
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.677	0.0	0.323
09	0.0	0.061	0.703	0.237
10	1.0	0.0	0.0	0.0
11	0.011	0.095	0.847	0.047
12	0.077	0.453	0.341	0.129
13	0.239	0.256	0.208	0.296

PWM

	A	C	G	T
01	-0.083	-0.057	0.035	0.095
02	-0.16	0.577	-0.14	-0.699
03	0.19	-0.127	0.585	-2.162
04	-2.271	0.838	-1.52	0.313
05	-6.262	-5.777	-6.636	1.385
06	1.385	-6.636	-6.636	-6.636
07	1.385	-6.636	-6.636	-6.636
08	-6.636	0.995	-6.636	0.256
09	-6.636	-1.414	1.033	-0.055
10	1.385	-6.636	-5.777	-6.636
11	-3.092	-0.967	1.22	-1.673
12	-1.178	0.594	0.309	-0.657
13	-0.045	0.024	-0.182	0.17

Standard thresholds

P-value	Threshold
0.001	2.52786
0.0005	4.61767
0.0001	7.506765