LHX9.H12INVITRO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX9.H12INVITRO.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	10
Consensus	nbTAATTdnn
GC content	28.0%
Information content (bits; total / per base)	9.595 / 0.96
Data sources	ChIP-Seq + HT-SELEX
Aligned words	9478

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)	0.79	0.818	0.659	0.709	0.709	0.721	1.846	1.89	83.432	120.721

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.964	0.949	0.872	0.86	0.732	0.746
Overall, 8 experiments	best	0.987	0.979	0.974	0.961	0.929	0.913
Methyl HT-SELEX, 3 experiments	median	0.967	0.95	0.93	0.904	0.812	0.804
Methyl HT-SELEX, 3 experiments	best	0.975	0.961	0.952	0.93	0.873	0.856
Non-Methyl HT-SELEX, 5 experiments	median	0.961	0.948	0.814	0.817	0.652	0.688
Non-Methyl HT-SELEX, 5 experiments	best	0.987	0.979	0.974	0.961	0.929	0.913

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.954	0.702	0.915	0.6
batch 2	0.791	0.684	0.676	0.535

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.0.PS.A.pcm
PWM	LHX9.H12INVITRO.0.PS.A.pwm
PFM	LHX9.H12INVITRO.0.PS.A.pfm
Alignment	LHX9.H12INVITRO.0.PS.A.words.tsv
Threshold to P-value map	LHX9.H12INVITRO.0.PS.A.thr
Motif in other formats
JASPAR format	LHX9.H12INVITRO.0.PS.A_jaspar_format.txt
MEME format	LHX9.H12INVITRO.0.PS.A_meme_format.meme
Transfac format	LHX9.H12INVITRO.0.PS.A_transfac_format.txt
Homer format	LHX9.H12INVITRO.0.PS.A_homer_format_0.001.txt LHX9.H12INVITRO.0.PS.A_homer_format_0.0005.txt LHX9.H12INVITRO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2757.75	2289.75	2539.75	1890.75
02	780.0	3611.0	1022.0	4065.0
03	0.0	125.0	23.0	9330.0
04	9478.0	0.0	0.0	0.0
05	9478.0	0.0	0.0	0.0
06	0.0	3.0	0.0	9475.0
07	31.0	376.0	1960.0	7111.0
08	4471.0	813.0	3335.0	859.0
09	1651.25	2218.25	3534.25	2074.25
10	2474.25	2242.25	2444.25	2317.25

PFM

	A	C	G	T
01	0.291	0.242	0.268	0.199
02	0.082	0.381	0.108	0.429
03	0.0	0.013	0.002	0.984
04	1.0	0.0	0.0	0.0
05	1.0	0.0	0.0	0.0
06	0.0	0.0	0.0	1.0
07	0.003	0.04	0.207	0.75
08	0.472	0.086	0.352	0.091
09	0.174	0.234	0.373	0.219
10	0.261	0.237	0.258	0.244

PWM

	A	C	G	T
01	0.152	-0.034	0.069	-0.225
02	-1.109	0.421	-0.84	0.539
03	-6.943	-2.925	-4.541	1.37
04	1.386	-6.943	-6.943	-6.943
05	1.386	-6.943	-6.943	-6.943
06	-6.943	-6.106	-6.943	1.385
07	-4.266	-1.836	-0.19	1.098
08	0.634	-1.068	0.342	-1.013
09	-0.361	-0.066	0.4	-0.133
10	0.043	-0.055	0.031	-0.022

Standard thresholds

P-value	Threshold
0.001	5.37877
0.0005	6.23445
0.0001	7.59426