LMX1B.H14RSNP.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LMX1B.H14RSNP.1.SM.B
Gene (human)	LMX1B (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lmx1b
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	12
Consensus	nYTAATTAAWWn
GC content	12.26%
Information content (bits; total / per base)	15.93 / 1.327
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9673
Previous names	LMX1B.H12RSNP.1.SM.B

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	1 (6)	0.701	0.72	0.542	0.607	0.636	0.653	1.743	1.776	30.796	40.699

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.977	0.96	0.968	0.949	0.888	0.88
Overall, 8 experiments	best	0.997	0.995	0.996	0.993	0.992	0.986
Methyl HT-SELEX, 2 experiments	median	0.997	0.994	0.994	0.99	0.968	0.964
Methyl HT-SELEX, 2 experiments	best	0.997	0.995	0.996	0.993	0.99	0.985
Non-Methyl HT-SELEX, 6 experiments	median	0.957	0.925	0.933	0.899	0.807	0.8
Non-Methyl HT-SELEX, 6 experiments	best	0.996	0.993	0.994	0.99	0.992	0.986

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.985	0.836	0.954	0.615
batch 2	0.799	0.663	0.804	0.602

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	LMX {3.1.5.6} (TFClass)
TFClass ID	TFClass: 3.1.5.6.2
HGNC	HGNC:6654
MGI	MGI:1100513
EntrezGene (human)	GeneID:4010 (SSTAR profile)
EntrezGene (mouse)	GeneID:16917 (SSTAR profile)
UniProt ID (human)	LMX1B_HUMAN
UniProt ID (mouse)	LMX1B_MOUSE
UniProt AC (human)	O60663 (TFClass)
UniProt AC (mouse)	O88609 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 1 mouse
HT-SELEX	6
Methyl-HT-SELEX	2
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	LMX1B.H14RSNP.1.SM.B.pcm
PWM	LMX1B.H14RSNP.1.SM.B.pwm
PFM	LMX1B.H14RSNP.1.SM.B.pfm
Threshold to P-value map	LMX1B.H14RSNP.1.SM.B.thr
Motif in other formats
JASPAR format	LMX1B.H14RSNP.1.SM.B_jaspar_format.txt
MEME format	LMX1B.H14RSNP.1.SM.B_meme_format.meme
Transfac format	LMX1B.H14RSNP.1.SM.B_transfac_format.txt
Homer format	LMX1B.H14RSNP.1.SM.B_homer_format_0.001.txt LMX1B.H14RSNP.1.SM.B_homer_format_0.0005.txt LMX1B.H14RSNP.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2379.0	1814.0	2214.0	3266.0
02	407.0	1810.0	1153.0	6303.0
03	9.0	89.0	1.0	9574.0
04	9673.0	0.0	0.0	0.0
05	9673.0	0.0	0.0	0.0
06	0.0	0.0	1.0	9672.0
07	0.0	0.0	0.0	9673.0
08	9669.0	1.0	3.0	0.0
09	9551.0	3.0	119.0	0.0
10	1178.0	813.0	478.0	7204.0
11	1055.5	793.5	937.5	6886.5
12	3083.75	2003.75	1996.75	2588.75

PFM

	A	C	G	T
01	0.246	0.188	0.229	0.338
02	0.042	0.187	0.119	0.652
03	0.001	0.009	0.0	0.99
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	0.0	0.0	0.0	1.0
08	1.0	0.0	0.0	0.0
09	0.987	0.0	0.012	0.0
10	0.122	0.084	0.049	0.745
11	0.109	0.082	0.097	0.712
12	0.319	0.207	0.206	0.268

PWM

	A	C	G	T
01	-0.016	-0.287	-0.088	0.3
02	-1.777	-0.289	-0.74	0.957
03	-5.367	-3.278	-6.6	1.375
04	1.386	-6.961	-6.961	-6.961
05	1.386	-6.961	-6.961	-6.961
06	-6.961	-6.961	-6.6	1.385
07	-6.961	-6.961	-6.961	1.386
08	1.385	-6.6	-6.125	-6.961
09	1.373	-6.125	-2.994	-6.961
10	-0.718	-1.088	-1.617	1.091
11	-0.828	-1.112	-0.946	1.046
12	0.243	-0.188	-0.191	0.068

Standard thresholds

P-value	Threshold
0.001	-0.745535
0.0005	1.01265
0.0001	4.660175