LMX1B.H14INVIVO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LMX1B.H14INVIVO.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	nYTAATTAAWKn
GC content	11.88%
Information content (bits; total / per base)	16.068 / 1.339
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9784
Previous names	LMX1B.H12INVIVO.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)	0.732	0.75	0.559	0.632	0.64	0.656	1.755	1.782	34.31	43.301

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.977	0.96	0.967	0.948	0.889	0.881
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	0.956	0.925	0.932	0.898	0.808	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	0.827	0.951	0.605
batch 2	0.797	0.66	0.796	0.594

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.H14INVIVO.1.SM.B.pcm
PWM	LMX1B.H14INVIVO.1.SM.B.pwm
PFM	LMX1B.H14INVIVO.1.SM.B.pfm
Threshold to P-value map	LMX1B.H14INVIVO.1.SM.B.thr
Motif in other formats
JASPAR format	LMX1B.H14INVIVO.1.SM.B_jaspar_format.txt
MEME format	LMX1B.H14INVIVO.1.SM.B_meme_format.meme
Transfac format	LMX1B.H14INVIVO.1.SM.B_transfac_format.txt
Homer format	LMX1B.H14INVIVO.1.SM.B_homer_format_0.001.txt LMX1B.H14INVIVO.1.SM.B_homer_format_0.0005.txt LMX1B.H14INVIVO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2496.75	2026.75	2008.75	3251.75
02	460.5	1871.5	810.5	6641.5
03	14.0	129.0	2.0	9639.0
04	9774.0	6.0	4.0	0.0
05	9784.0	0.0	0.0	0.0
06	0.0	1.0	1.0	9782.0
07	0.0	0.0	0.0	9784.0
08	9784.0	0.0	0.0	0.0
09	9665.0	18.0	101.0	0.0
10	1015.0	837.0	390.0	7542.0
11	859.25	848.25	1048.25	7028.25
12	2852.0	1748.0	2095.0	3089.0

PFM

	A	C	G	T
01	0.255	0.207	0.205	0.332
02	0.047	0.191	0.083	0.679
03	0.001	0.013	0.0	0.985
04	0.999	0.001	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	0.988	0.002	0.01	0.0
10	0.104	0.086	0.04	0.771
11	0.088	0.087	0.107	0.718
12	0.291	0.179	0.214	0.316

PWM

	A	C	G	T
01	0.021	-0.188	-0.197	0.285
02	-1.666	-0.267	-1.103	0.998
03	-5.012	-2.926	-6.345	1.371
04	1.385	-5.687	-5.963	-6.971
05	1.386	-6.971	-6.971	-6.971
06	-6.971	-6.61	-6.61	1.385
07	-6.971	-6.971	-6.971	1.386
08	1.386	-6.971	-6.971	-6.971
09	1.373	-4.793	-3.166	-6.971
10	-0.878	-1.071	-1.831	1.125
11	-1.044	-1.057	-0.846	1.055
12	0.153	-0.336	-0.155	0.233

Standard thresholds

P-value	Threshold
0.001	-0.65738
0.0005	1.11878
0.0001	4.774975