LHX2.H12INVIVO.1.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX2.H12INVIVO.1.S.C
Gene (human)	LHX2 (GeneCards)
Gene synonyms (human)	LH2
Gene (mouse)	Lhx2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	C

Motif length	19
Consensus	nhhWWWdnvYTAATTAvnn
GC content	26.26%
Information content (bits; total / per base)	15.479 / 0.815
Data sources	HT-SELEX
Aligned words	2014

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)	0.786	0.795	0.576	0.581	0.807	0.821	2.36	2.385	89.699	97.018
Mouse	9 (53)	0.851	0.922	0.677	0.822	0.777	0.883	2.558	3.172	126.222	203.678

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.769	0.746	0.64	0.643	0.569	0.584
Non-Methyl HT-SELEX, 2 experiments	best	0.867	0.849	0.693	0.704	0.592	0.619

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.1.S.C.pcm
PWM	LHX2.H12INVIVO.1.S.C.pwm
PFM	LHX2.H12INVIVO.1.S.C.pfm
Alignment	LHX2.H12INVIVO.1.S.C.words.tsv
Threshold to P-value map	LHX2.H12INVIVO.1.S.C.thr
Motif in other formats
JASPAR format	LHX2.H12INVIVO.1.S.C_jaspar_format.txt
MEME format	LHX2.H12INVIVO.1.S.C_meme_format.meme
Transfac format	LHX2.H12INVIVO.1.S.C_transfac_format.txt
Homer format	LHX2.H12INVIVO.1.S.C_homer_format_0.001.txt LHX2.H12INVIVO.1.S.C_homer_format_0.0005.txt LHX2.H12INVIVO.1.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	569.75	461.75	291.75	690.75
02	517.0	492.0	121.0	884.0
03	1097.0	314.0	104.0	499.0
04	1351.0	81.0	121.0	461.0
05	553.0	59.0	103.0	1299.0
06	391.0	110.0	167.0	1346.0
07	1051.0	161.0	285.0	517.0
08	711.0	439.0	502.0	362.0
09	577.0	387.0	873.0	177.0
10	87.0	1193.0	200.0	534.0
11	0.0	2.0	0.0	2012.0
12	2010.0	4.0	0.0	0.0
13	2014.0	0.0	0.0	0.0
14	0.0	0.0	0.0	2014.0
15	1.0	1.0	20.0	1992.0
16	1697.0	1.0	315.0	1.0
17	607.0	282.0	1031.0	94.0
18	304.75	565.75	483.75	659.75
19	552.5	387.5	488.5	585.5

PFM

	A	C	G	T
01	0.283	0.229	0.145	0.343
02	0.257	0.244	0.06	0.439
03	0.545	0.156	0.052	0.248
04	0.671	0.04	0.06	0.229
05	0.275	0.029	0.051	0.645
06	0.194	0.055	0.083	0.668
07	0.522	0.08	0.142	0.257
08	0.353	0.218	0.249	0.18
09	0.286	0.192	0.433	0.088
10	0.043	0.592	0.099	0.265
11	0.0	0.001	0.0	0.999
12	0.998	0.002	0.0	0.0
13	1.0	0.0	0.0	0.0
14	0.0	0.0	0.0	1.0
15	0.0	0.0	0.01	0.989
16	0.843	0.0	0.156	0.0
17	0.301	0.14	0.512	0.047
18	0.151	0.281	0.24	0.328
19	0.274	0.192	0.243	0.291

PWM

	A	C	G	T
01	0.123	-0.086	-0.543	0.315
02	0.026	-0.023	-1.414	0.561
03	0.777	-0.47	-1.563	-0.009
04	0.985	-1.808	-1.414	-0.088
05	0.093	-2.116	-1.572	0.945
06	-0.252	-1.508	-1.096	0.981
07	0.734	-1.132	-0.566	0.026
08	0.344	-0.137	-0.003	-0.328
09	0.136	-0.262	0.549	-1.039
10	-1.738	0.86	-0.918	0.059
11	-5.582	-4.864	-5.582	1.382
12	1.381	-4.45	-5.582	-5.582
13	1.383	-5.582	-5.582	-5.582
14	-5.582	-5.582	-5.582	1.383
15	-5.16	-5.16	-3.139	1.372
16	1.212	-5.16	-0.467	-5.16
17	0.186	-0.577	0.715	-1.662
18	-0.5	0.116	-0.04	0.269
19	0.093	-0.261	-0.03	0.15

Standard thresholds

P-value	Threshold
0.001	1.46291
0.0005	2.97301
0.0001	6.32036