LHX9.H12INVITRO.1.M.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX9.H12INVITRO.1.M.B
Gene (human)	LHX9 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lhx9
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	12
Consensus	nvYTAAYGAKbn
GC content	36.81%
Information content (bits; total / per base)	11.441 / 0.953
Data sources	Methyl-HT-SELEX
Aligned words	911

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)	0.782	0.811	0.653	0.694	0.708	0.715	1.911	1.959	67.347	109.174

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.931	0.896	0.857	0.828	0.751	0.743
Overall, 8 experiments	best	0.975	0.958	0.963	0.941	0.93	0.904
Methyl HT-SELEX, 3 experiments	median	0.97	0.95	0.949	0.923	0.877	0.856
Methyl HT-SELEX, 3 experiments	best	0.975	0.958	0.963	0.941	0.93	0.904
Non-Methyl HT-SELEX, 5 experiments	median	0.909	0.872	0.788	0.766	0.651	0.666
Non-Methyl HT-SELEX, 5 experiments	best	0.964	0.937	0.941	0.91	0.88	0.851

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.784	0.264	0.768	0.439
batch 2	0.619	0.441	0.487	0.33

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.H12INVITRO.1.M.B.pcm
PWM	LHX9.H12INVITRO.1.M.B.pwm
PFM	LHX9.H12INVITRO.1.M.B.pfm
Alignment	LHX9.H12INVITRO.1.M.B.words.tsv
Threshold to P-value map	LHX9.H12INVITRO.1.M.B.thr
Motif in other formats
JASPAR format	LHX9.H12INVITRO.1.M.B_jaspar_format.txt
MEME format	LHX9.H12INVITRO.1.M.B_meme_format.meme
Transfac format	LHX9.H12INVITRO.1.M.B_transfac_format.txt
Homer format	LHX9.H12INVITRO.1.M.B_homer_format_0.001.txt LHX9.H12INVITRO.1.M.B_homer_format_0.0005.txt LHX9.H12INVITRO.1.M.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	316.0	247.0	166.0	182.0
02	358.0	94.0	400.0	59.0
03	42.0	251.0	56.0	562.0
04	0.0	1.0	5.0	905.0
05	909.0	0.0	2.0	0.0
06	904.0	1.0	6.0	0.0
07	0.0	497.0	6.0	408.0
08	0.0	0.0	542.0	369.0
09	887.0	3.0	21.0	0.0
10	63.0	78.0	621.0	149.0
11	105.5	372.5	259.5	173.5
12	220.25	171.25	224.25	295.25

PFM

	A	C	G	T
01	0.347	0.271	0.182	0.2
02	0.393	0.103	0.439	0.065
03	0.046	0.276	0.061	0.617
04	0.0	0.001	0.005	0.993
05	0.998	0.0	0.002	0.0
06	0.992	0.001	0.007	0.0
07	0.0	0.546	0.007	0.448
08	0.0	0.0	0.595	0.405
09	0.974	0.003	0.023	0.0
10	0.069	0.086	0.682	0.164
11	0.116	0.409	0.285	0.19
12	0.242	0.188	0.246	0.324

PWM

	A	C	G	T
01	0.325	0.081	-0.314	-0.222
02	0.45	-0.874	0.56	-1.33
03	-1.658	0.097	-1.38	0.899
04	-4.903	-4.441	-3.533	1.374
05	1.379	-4.903	-4.126	-4.903
06	1.373	-4.441	-3.394	-4.903
07	-4.903	0.776	-3.394	0.58
08	-4.903	-4.903	0.863	0.48
09	1.354	-3.887	-2.313	-4.903
10	-1.266	-1.057	0.998	-0.42
11	-0.761	0.489	0.13	-0.27
12	-0.033	-0.283	-0.015	0.258

Standard thresholds

P-value	Threshold
0.001	3.997465
0.0005	5.41878
0.0001	7.646965