LHX6.H12RSNP.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX6.H12RSNP.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	12
Consensus	nSTAATTARbbn
GC content	32.51%
Information content (bits; total / per base)	11.985 / 0.999
Data sources	HT-SELEX
Aligned words	1517

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)	0.815	0.874	0.639	0.729	0.725	0.841	1.83	2.545	109.731	153.699

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.821	0.807	0.774	0.768	0.748	0.743
Overall, 4 experiments	best	0.988	0.982	0.98	0.969	0.971	0.955
Methyl HT-SELEX, 1 experiments	median	0.987	0.98	0.977	0.964	0.961	0.943
Methyl HT-SELEX, 1 experiments	best	0.987	0.98	0.977	0.964	0.961	0.943
Non-Methyl HT-SELEX, 3 experiments	median	0.654	0.635	0.571	0.573	0.534	0.542
Non-Methyl HT-SELEX, 3 experiments	best	0.988	0.982	0.98	0.969	0.971	0.955

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.955	0.83	0.933	0.592

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.H12RSNP.1.S.B.pcm
PWM	LHX6.H12RSNP.1.S.B.pwm
PFM	LHX6.H12RSNP.1.S.B.pfm
Alignment	LHX6.H12RSNP.1.S.B.words.tsv
Threshold to P-value map	LHX6.H12RSNP.1.S.B.thr
Motif in other formats
JASPAR format	LHX6.H12RSNP.1.S.B_jaspar_format.txt
MEME format	LHX6.H12RSNP.1.S.B_meme_format.meme
Transfac format	LHX6.H12RSNP.1.S.B_transfac_format.txt
Homer format	LHX6.H12RSNP.1.S.B_homer_format_0.001.txt LHX6.H12RSNP.1.S.B_homer_format_0.0005.txt LHX6.H12RSNP.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	433.75	353.75	386.75	342.75
02	7.5	642.5	604.5	262.5
03	0.0	138.0	0.0	1379.0
04	1517.0	0.0	0.0	0.0
05	1517.0	0.0	0.0	0.0
06	0.0	0.0	0.0	1517.0
07	0.0	421.0	0.0	1096.0
08	1517.0	0.0	0.0	0.0
09	695.0	40.0	613.0	169.0
10	58.0	557.0	457.0	445.0
11	212.5	427.5	558.5	318.5
12	409.0	352.0	367.0	389.0

PFM

	A	C	G	T
01	0.286	0.233	0.255	0.226
02	0.005	0.424	0.398	0.173
03	0.0	0.091	0.0	0.909
04	1.0	0.0	0.0	0.0
05	1.0	0.0	0.0	0.0
06	0.0	0.0	0.0	1.0
07	0.0	0.278	0.0	0.722
08	1.0	0.0	0.0	0.0
09	0.458	0.026	0.404	0.111
10	0.038	0.367	0.301	0.293
11	0.14	0.282	0.368	0.21
12	0.27	0.232	0.242	0.256

PWM

	A	C	G	T
01	0.134	-0.069	0.019	-0.101
02	-3.71	0.525	0.464	-0.366
03	-5.338	-1.003	-5.338	1.287
04	1.383	-5.338	-5.338	-5.338
05	1.383	-5.338	-5.338	-5.338
06	-5.338	-5.338	-5.338	1.383
07	-5.338	0.104	-5.338	1.058
08	1.383	-5.338	-5.338	-5.338
09	0.604	-2.209	0.478	-0.802
10	-1.851	0.383	0.186	0.159
11	-0.575	0.119	0.386	-0.174
12	0.075	-0.074	-0.033	0.025

Standard thresholds

P-value	Threshold
0.001	2.649685
0.0005	4.815385
0.0001	7.97069