LHX9.H12CORE.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX9.H12CORE.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	32.6%
Information content (bits; total / per base)	12.411 / 1.034
Data sources	ChIP-Seq + HT-SELEX
Aligned words	6527

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)	0.793	0.823	0.648	0.705	0.713	0.723	1.874	1.919	97.62	136.013

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.961	0.941	0.872	0.857	0.736	0.746
Overall, 8 experiments	best	0.985	0.975	0.974	0.96	0.932	0.915
Methyl HT-SELEX, 3 experiments	median	0.965	0.944	0.929	0.902	0.818	0.806
Methyl HT-SELEX, 3 experiments	best	0.972	0.953	0.952	0.928	0.879	0.858
Non-Methyl HT-SELEX, 5 experiments	median	0.956	0.937	0.815	0.812	0.655	0.687
Non-Methyl HT-SELEX, 5 experiments	best	0.985	0.975	0.974	0.96	0.932	0.915

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.971	0.797	0.936	0.583
batch 2	0.751	0.632	0.702	0.553

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.H12CORE.0.PS.A.pcm
PWM	LHX9.H12CORE.0.PS.A.pwm
PFM	LHX9.H12CORE.0.PS.A.pfm
Alignment	LHX9.H12CORE.0.PS.A.words.tsv
Threshold to P-value map	LHX9.H12CORE.0.PS.A.thr
Motif in other formats
JASPAR format	LHX9.H12CORE.0.PS.A_jaspar_format.txt
MEME format	LHX9.H12CORE.0.PS.A_meme_format.meme
Transfac format	LHX9.H12CORE.0.PS.A_transfac_format.txt
Homer format	LHX9.H12CORE.0.PS.A_homer_format_0.001.txt LHX9.H12CORE.0.PS.A_homer_format_0.0005.txt LHX9.H12CORE.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1594.5	1512.5	1364.5	2055.5
02	1285.5	2510.5	1304.5	1426.5
03	2139.0	1487.0	2489.0	412.0
04	30.0	3662.0	275.0	2560.0
05	0.0	2.0	0.0	6525.0
06	6527.0	0.0	0.0	0.0
07	6527.0	0.0	0.0	0.0
08	0.0	0.0	0.0	6527.0
09	0.0	0.0	270.0	6257.0
10	4382.0	4.0	2140.0	1.0
11	638.5	1134.5	4204.5	549.5
12	1606.25	1566.25	1605.25	1749.25

PFM

	A	C	G	T
01	0.244	0.232	0.209	0.315
02	0.197	0.385	0.2	0.219
03	0.328	0.228	0.381	0.063
04	0.005	0.561	0.042	0.392
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	0.041	0.959
10	0.671	0.001	0.328	0.0
11	0.098	0.174	0.644	0.084
12	0.246	0.24	0.246	0.268

PWM

	A	C	G	T
01	-0.023	-0.076	-0.179	0.231
02	-0.238	0.43	-0.223	-0.134
03	0.27	-0.093	0.422	-1.372
04	-3.927	0.808	-1.774	0.45
05	-6.612	-5.965	-6.612	1.385
06	1.385	-6.612	-6.612	-6.612
07	1.385	-6.612	-6.612	-6.612
08	-6.612	-6.612	-6.612	1.385
09	-6.612	-6.612	-1.792	1.343
10	0.987	-5.575	0.271	-6.237
11	-0.936	-0.363	0.946	-1.086
12	-0.016	-0.041	-0.016	0.069

Standard thresholds

P-value	Threshold
0.001	1.744165
0.0005	4.20246
0.0001	7.756065