LMX1B.H14INVIVO.0.P.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LMX1B.H14INVIVO.0.P.C
Gene (human)	LMX1B (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lmx1b
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	C

Motif length	8
Consensus	YMATdAAA
GC content	12.93%
Information content (bits; total / per base)	10.032 / 1.254
Data sources	ChIP-Seq
Aligned words	1008
Previous names	LMX1B.H12INVIVO.0.P.C

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)	0.733	0.752	0.579	0.658	0.731	0.747	2.017	2.042	38.092	44.658

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.958	0.939	0.905	0.88	0.823	0.805
Overall, 8 experiments	best	0.994	0.988	0.986	0.979	0.954	0.94
Methyl HT-SELEX, 2 experiments	median	0.993	0.987	0.958	0.949	0.913	0.896
Methyl HT-SELEX, 2 experiments	best	0.994	0.988	0.965	0.956	0.944	0.923
Non-Methyl HT-SELEX, 6 experiments	median	0.911	0.878	0.848	0.805	0.744	0.725
Non-Methyl HT-SELEX, 6 experiments	best	0.993	0.988	0.986	0.979	0.954	0.94

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.821	0.272	0.881	0.593
batch 2	0.694	0.439	0.78	0.553

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.0.P.C.pcm
PWM	LMX1B.H14INVIVO.0.P.C.pwm
PFM	LMX1B.H14INVIVO.0.P.C.pfm
Threshold to P-value map	LMX1B.H14INVIVO.0.P.C.thr
Motif in other formats
JASPAR format	LMX1B.H14INVIVO.0.P.C_jaspar_format.txt
MEME format	LMX1B.H14INVIVO.0.P.C_meme_format.meme
Transfac format	LMX1B.H14INVIVO.0.P.C_transfac_format.txt
Homer format	LMX1B.H14INVIVO.0.P.C_homer_format_0.001.txt LMX1B.H14INVIVO.0.P.C_homer_format_0.0005.txt LMX1B.H14INVIVO.0.P.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	148.0	227.0	12.0	621.0
02	783.0	130.0	36.0	59.0
03	989.0	12.0	6.0	1.0
04	8.25	7.25	27.25	965.25
05	194.25	39.25	361.25	413.25
06	977.25	3.25	21.25	6.25
07	957.25	15.25	34.25	1.25
08	874.25	43.25	67.25	23.25

PFM

	A	C	G	T
01	0.147	0.225	0.012	0.616
02	0.777	0.129	0.036	0.059
03	0.981	0.012	0.006	0.001
04	0.008	0.007	0.027	0.958
05	0.193	0.039	0.358	0.41
06	0.969	0.003	0.021	0.006
07	0.95	0.015	0.034	0.001
08	0.867	0.043	0.067	0.023

PWM

	A	C	G	T
01	-0.527	-0.104	-2.917	0.898
02	1.129	-0.656	-1.906	-1.43
03	1.362	-2.917	-3.491	-4.532
04	-3.236	-3.341	-2.17	1.338
05	-0.258	-1.823	0.358	0.492
06	1.35	-3.931	-2.402	-3.459
07	1.33	-2.704	-1.953	-4.445
08	1.239	-1.73	-1.302	-2.318

Standard thresholds

P-value	Threshold
0.001	4.782235
0.0005	5.589145
0.0001	7.499125