LHX2.H12INVIVO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX2.H12INVIVO.0.PS.A
Gene (human)	LHX2 (GeneCards)
Gene synonyms (human)	LH2
Gene (mouse)	Lhx2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	11
Consensus	nnYTAATKASn
GC content	31.46%
Information content (bits; total / per base)	10.573 / 0.961
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1003

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 (6)	0.853	0.866	0.716	0.728	0.845	0.859	2.628	2.695	170.919	194.081
Mouse	9 (53)	0.892	0.965	0.779	0.926	0.842	0.93	2.719	3.506	191.469	386.854

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.76	0.723	0.647	0.638	0.571	0.582
Non-Methyl HT-SELEX, 2 experiments	best	0.855	0.819	0.704	0.699	0.598	0.617

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: 3.1.5.3.1
HGNC	HGNC:6594
MGI	MGI:96785
EntrezGene (human)	GeneID:9355 (SSTAR profile)
EntrezGene (mouse)	GeneID:16870 (SSTAR profile)
UniProt ID (human)	LHX2_HUMAN
UniProt ID (mouse)	LHX2_MOUSE
UniProt AC (human)	P50458 (TFClass)
UniProt AC (mouse)	Q9Z0S2 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 9 mouse
HT-SELEX	2
Methyl-HT-SELEX	0

PCM	LHX2.H12INVIVO.0.PS.A.pcm
PWM	LHX2.H12INVIVO.0.PS.A.pwm
PFM	LHX2.H12INVIVO.0.PS.A.pfm
Alignment	LHX2.H12INVIVO.0.PS.A.words.tsv
Threshold to P-value map	LHX2.H12INVIVO.0.PS.A.thr
Motif in other formats
JASPAR format	LHX2.H12INVIVO.0.PS.A_jaspar_format.txt
MEME format	LHX2.H12INVIVO.0.PS.A_meme_format.meme
Transfac format	LHX2.H12INVIVO.0.PS.A_transfac_format.txt
Homer format	LHX2.H12INVIVO.0.PS.A_homer_format_0.001.txt LHX2.H12INVIVO.0.PS.A_homer_format_0.0005.txt LHX2.H12INVIVO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	238.0	210.0	178.0	377.0
02	196.0	239.0	281.0	287.0
03	148.0	338.0	22.0	495.0
04	12.0	4.0	3.0	984.0
05	974.0	10.0	15.0	4.0
06	997.0	4.0	1.0	1.0
07	1.0	2.0	2.0	998.0
08	18.0	25.0	364.0	596.0
09	652.0	0.0	349.0	2.0
10	52.0	217.0	674.0	60.0
11	177.0	338.0	195.0	293.0

PFM

	A	C	G	T
01	0.237	0.209	0.177	0.376
02	0.195	0.238	0.28	0.286
03	0.148	0.337	0.022	0.494
04	0.012	0.004	0.003	0.981
05	0.971	0.01	0.015	0.004
06	0.994	0.004	0.001	0.001
07	0.001	0.002	0.002	0.995
08	0.018	0.025	0.363	0.594
09	0.65	0.0	0.348	0.002
10	0.052	0.216	0.672	0.06
11	0.176	0.337	0.194	0.292

PWM

	A	C	G	T
01	-0.052	-0.176	-0.34	0.405
02	-0.244	-0.048	0.113	0.134
03	-0.523	0.297	-2.365	0.677
04	-2.912	-3.786	-3.978	1.362
05	1.352	-3.069	-2.714	-3.786
06	1.375	-3.786	-4.528	-4.528
07	-4.528	-4.216	-4.216	1.376
08	-2.549	-2.246	0.371	0.862
09	0.951	-4.985	0.329	-4.216
10	-1.547	-0.143	0.984	-1.409
11	-0.345	0.297	-0.25	0.155

Standard thresholds

P-value	Threshold
0.001	4.390935
0.0005	5.667205
0.0001	7.818605