LHX6.H12INVITRO.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX6.H12INVITRO.1.S.B
Gene (human)	LHX6 (GeneCards)
Gene synonyms (human)	LHX6.1
Gene (mouse)	Lhx6
Gene synonyms (mouse)	Lhx6.1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	10
Consensus	nbAATTAvbn
GC content	32.51%
Information content (bits; total / per base)	8.242 / 0.824
Data sources	HT-SELEX
Aligned words	7888

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)	0.805	0.898	0.629	0.784	0.703	0.83	1.648	2.512	107.877	150.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.825	0.816	0.781	0.778	0.755	0.753
Overall, 4 experiments	best	0.996	0.993	0.987	0.982	0.98	0.969
Methyl HT-SELEX, 1 experiments	median	0.994	0.99	0.985	0.977	0.972	0.96
Methyl HT-SELEX, 1 experiments	best	0.994	0.99	0.985	0.977	0.972	0.96
Non-Methyl HT-SELEX, 3 experiments	median	0.657	0.642	0.578	0.579	0.537	0.546
Non-Methyl HT-SELEX, 3 experiments	best	0.996	0.993	0.987	0.982	0.98	0.969

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.944	0.789	0.922	0.622

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.H12INVITRO.1.S.B.pcm
PWM	LHX6.H12INVITRO.1.S.B.pwm
PFM	LHX6.H12INVITRO.1.S.B.pfm
Alignment	LHX6.H12INVITRO.1.S.B.words.tsv
Threshold to P-value map	LHX6.H12INVITRO.1.S.B.thr
Motif in other formats
JASPAR format	LHX6.H12INVITRO.1.S.B_jaspar_format.txt
MEME format	LHX6.H12INVITRO.1.S.B_meme_format.meme
Transfac format	LHX6.H12INVITRO.1.S.B_transfac_format.txt
Homer format	LHX6.H12INVITRO.1.S.B_homer_format_0.001.txt LHX6.H12INVITRO.1.S.B_homer_format_0.0005.txt LHX6.H12INVITRO.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1708.0	2073.0	1960.0	2147.0
02	902.25	2034.25	921.25	4030.25
03	6171.0	1392.0	274.0	51.0
04	7724.0	150.0	14.0	0.0
05	0.0	0.0	0.0	7888.0
06	0.0	2636.0	0.0	5252.0
07	7557.0	318.0	3.0	10.0
08	2247.0	1662.0	3015.0	964.0
09	824.25	2810.25	2136.25	2117.25
10	1684.25	2035.25	2210.25	1958.25

PFM

	A	C	G	T
01	0.217	0.263	0.248	0.272
02	0.114	0.258	0.117	0.511
03	0.782	0.176	0.035	0.006
04	0.979	0.019	0.002	0.0
05	0.0	0.0	0.0	1.0
06	0.0	0.334	0.0	0.666
07	0.958	0.04	0.0	0.001
08	0.285	0.211	0.382	0.122
09	0.104	0.356	0.271	0.268
10	0.214	0.258	0.28	0.248

PWM

	A	C	G	T
01	-0.144	0.05	-0.006	0.085
02	-0.781	0.031	-0.76	0.714
03	1.14	-0.348	-1.967	-3.613
04	1.364	-2.562	-4.8	-6.78
05	-6.78	-6.78	-6.78	1.385
06	-6.78	0.29	-6.78	0.979
07	1.343	-1.819	-5.931	-5.083
08	0.13	-0.171	0.424	-0.715
09	-0.871	0.354	0.08	0.071
10	-0.158	0.032	0.114	-0.007

Standard thresholds

P-value	Threshold
0.001	5.592505
0.0005	6.142875
0.0001	7.08708