LHX6.H12INVITRO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX6.H12INVITRO.0.P.B
Gene (human)	LHX6 (GeneCards)
Gene synonyms (human)	LHX6.1
Gene (mouse)	Lhx6
Gene synonyms (mouse)	Lhx6.1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	10
Consensus	bYAATCARnn
GC content	40.21%
Information content (bits; total / per base)	10.153 / 1.015
Data sources	ChIP-Seq
Aligned words	1014

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
Mouse	2 (12)	0.874	0.927	0.804	0.847	0.804	0.842	2.412	2.514	163.245	199.131

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.81	0.787	0.77	0.757	0.748	0.738
Overall, 4 experiments	best	0.985	0.975	0.978	0.964	0.97	0.952
Methyl HT-SELEX, 1 experiments	median	0.978	0.964	0.971	0.952	0.962	0.938
Methyl HT-SELEX, 1 experiments	best	0.978	0.964	0.971	0.952	0.962	0.938
Non-Methyl HT-SELEX, 3 experiments	median	0.642	0.61	0.569	0.563	0.534	0.537
Non-Methyl HT-SELEX, 3 experiments	best	0.985	0.975	0.978	0.964	0.97	0.952

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.91	0.73	0.902	0.577

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	LHX6-like {3.1.5.5} (TFClass)
TFClass ID	TFClass: 3.1.5.5.1
HGNC	HGNC:21735
MGI	MGI:1306803
EntrezGene (human)	GeneID:26468 (SSTAR profile)
EntrezGene (mouse)	GeneID:16874 (SSTAR profile)
UniProt ID (human)	LHX6_HUMAN
UniProt ID (mouse)	LHX6_MOUSE
UniProt AC (human)	Q9UPM6 (TFClass)
UniProt AC (mouse)	Q9R1R0 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 2 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	LHX6.H12INVITRO.0.P.B.pcm
PWM	LHX6.H12INVITRO.0.P.B.pwm
PFM	LHX6.H12INVITRO.0.P.B.pfm
Alignment	LHX6.H12INVITRO.0.P.B.words.tsv
Threshold to P-value map	LHX6.H12INVITRO.0.P.B.thr
Motif in other formats
JASPAR format	LHX6.H12INVITRO.0.P.B_jaspar_format.txt
MEME format	LHX6.H12INVITRO.0.P.B_meme_format.meme
Transfac format	LHX6.H12INVITRO.0.P.B_transfac_format.txt
Homer format	LHX6.H12INVITRO.0.P.B_homer_format_0.001.txt LHX6.H12INVITRO.0.P.B_homer_format_0.0005.txt LHX6.H12INVITRO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	76.0	307.0	478.0	153.0
02	43.0	464.0	6.0	501.0
03	931.0	77.0	1.0	5.0
04	988.0	4.0	7.0	15.0
05	1.0	0.0	1.0	1012.0
06	2.0	870.0	36.0	106.0
07	1008.0	0.0	0.0	6.0
08	263.0	112.0	595.0	44.0
09	323.0	269.0	270.0	152.0
10	260.0	251.0	329.0	174.0

PFM

	A	C	G	T
01	0.075	0.303	0.471	0.151
02	0.042	0.458	0.006	0.494
03	0.918	0.076	0.001	0.005
04	0.974	0.004	0.007	0.015
05	0.001	0.0	0.001	0.998
06	0.002	0.858	0.036	0.105
07	0.994	0.0	0.0	0.006
08	0.259	0.11	0.587	0.043
09	0.319	0.265	0.266	0.15
10	0.256	0.248	0.324	0.172

PWM

	A	C	G	T
01	-1.189	0.19	0.631	-0.5
02	-1.742	0.601	-3.497	0.678
03	1.296	-1.176	-4.538	-3.636
04	1.355	-3.796	-3.375	-2.725
05	-4.538	-4.994	-4.538	1.379
06	-4.226	1.228	-1.912	-0.863
07	1.375	-4.994	-4.994	-3.497
08	0.037	-0.808	0.849	-1.719
09	0.241	0.059	0.063	-0.507
10	0.025	-0.01	0.259	-0.373

Standard thresholds

P-value	Threshold
0.001	4.75783
0.0005	5.843045
0.0001	7.71308