LHX9.H12RSNP.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX9.H12RSNP.0.PS.A
Gene (human)	LHX9 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lhx9
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	nnvYTAATTASn
GC content	29.83%
Information content (bits; total / per base)	13.012 / 1.084
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1985

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
Human	1 (5)	0.783	0.813	0.633	0.688	0.692	0.705	1.816	1.85	94.585	123.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.958	0.937	0.868	0.853	0.731	0.742
Overall, 8 experiments	best	0.984	0.973	0.972	0.956	0.93	0.912
Methyl HT-SELEX, 3 experiments	median	0.963	0.94	0.928	0.899	0.814	0.802
Methyl HT-SELEX, 3 experiments	best	0.971	0.95	0.95	0.924	0.876	0.855
Non-Methyl HT-SELEX, 5 experiments	median	0.953	0.933	0.808	0.807	0.649	0.682
Non-Methyl HT-SELEX, 5 experiments	best	0.984	0.973	0.972	0.956	0.93	0.912

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.967	0.79	0.937	0.577
batch 2	0.756	0.659	0.72	0.593

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	LHX2-like {3.1.5.3} (TFClass)
TFClass ID	TFClass: 3.1.5.3.2
HGNC	HGNC:14222
MGI	MGI:1316721
EntrezGene (human)	GeneID:56956 (SSTAR profile)
EntrezGene (mouse)	GeneID:16876 (SSTAR profile)
UniProt ID (human)	LHX9_HUMAN
UniProt ID (mouse)	LHX9_MOUSE
UniProt AC (human)	Q9NQ69 (TFClass)
UniProt AC (mouse)	Q9WUH2 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	5
Methyl-HT-SELEX	3

PCM	LHX9.H12RSNP.0.PS.A.pcm
PWM	LHX9.H12RSNP.0.PS.A.pwm
PFM	LHX9.H12RSNP.0.PS.A.pfm
Alignment	LHX9.H12RSNP.0.PS.A.words.tsv
Threshold to P-value map	LHX9.H12RSNP.0.PS.A.thr
Motif in other formats
JASPAR format	LHX9.H12RSNP.0.PS.A_jaspar_format.txt
MEME format	LHX9.H12RSNP.0.PS.A_meme_format.meme
Transfac format	LHX9.H12RSNP.0.PS.A_transfac_format.txt
Homer format	LHX9.H12RSNP.0.PS.A_homer_format_0.001.txt LHX9.H12RSNP.0.PS.A_homer_format_0.0005.txt LHX9.H12RSNP.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	452.5	492.5	386.5	653.5
02	470.5	778.5	340.5	395.5
03	825.0	439.0	644.0	77.0
04	13.0	1098.0	21.0	853.0
05	0.0	0.0	0.0	1985.0
06	1985.0	0.0	0.0	0.0
07	1985.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1985.0
09	0.0	0.0	25.0	1960.0
10	1583.0	1.0	400.0	1.0
11	249.25	268.25	1317.25	150.25
12	491.25	459.25	434.25	600.25

PFM

	A	C	G	T
01	0.228	0.248	0.195	0.329
02	0.237	0.392	0.172	0.199
03	0.416	0.221	0.324	0.039
04	0.007	0.553	0.011	0.43
05	0.0	0.0	0.0	1.0
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.0	0.013	0.987
10	0.797	0.001	0.202	0.001
11	0.126	0.135	0.664	0.076
12	0.247	0.231	0.219	0.302

PWM

	A	C	G	T
01	-0.092	-0.008	-0.249	0.274
02	-0.053	0.449	-0.375	-0.226
03	0.507	-0.122	0.26	-1.843
04	-3.51	0.792	-3.08	0.54
05	-5.57	-5.57	-5.57	1.383
06	1.383	-5.57	-5.57	-5.57
07	1.383	-5.57	-5.57	-5.57
08	-5.57	-5.57	-5.57	1.383
09	-5.57	-5.57	-2.919	1.371
10	1.157	-5.147	-0.215	-5.147
11	-0.685	-0.612	0.974	-1.186
12	-0.01	-0.077	-0.133	0.19

Standard thresholds

P-value	Threshold
0.001	2.26572
0.0005	3.53583
0.0001	7.70884