LMX1B.H14RSNP.0.P.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LMX1B.H14RSNP.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	YAATdAAR
GC content	15.1%
Information content (bits; total / per base)	9.921 / 1.24
Data sources	ChIP-Seq
Aligned words	1007
Previous names	LMX1B.H12RSNP.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	0.755	0.584	0.656	0.733	0.743	2.024	2.081	41.886	48.444

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.941	0.905	0.919	0.881	0.847	0.819
Overall, 8 experiments	best	0.984	0.964	0.979	0.96	0.96	0.939
Methyl HT-SELEX, 2 experiments	median	0.979	0.958	0.965	0.945	0.922	0.9
Methyl HT-SELEX, 2 experiments	best	0.984	0.964	0.973	0.954	0.95	0.927
Non-Methyl HT-SELEX, 6 experiments	median	0.904	0.85	0.872	0.816	0.778	0.748
Non-Methyl HT-SELEX, 6 experiments	best	0.975	0.954	0.979	0.96	0.96	0.939

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.851	0.256	0.882	0.592
batch 2	0.682	0.445	0.775	0.548

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.0.P.C.pcm
PWM	LMX1B.H14RSNP.0.P.C.pwm
PFM	LMX1B.H14RSNP.0.P.C.pfm
Threshold to P-value map	LMX1B.H14RSNP.0.P.C.thr
Motif in other formats
JASPAR format	LMX1B.H14RSNP.0.P.C_jaspar_format.txt
MEME format	LMX1B.H14RSNP.0.P.C_meme_format.meme
Transfac format	LMX1B.H14RSNP.0.P.C_transfac_format.txt
Homer format	LMX1B.H14RSNP.0.P.C_homer_format_0.001.txt LMX1B.H14RSNP.0.P.C_homer_format_0.0005.txt LMX1B.H14RSNP.0.P.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	141.0	176.0	19.0	671.0
02	943.0	11.0	38.0	15.0
03	985.0	9.0	6.0	7.0
04	9.25	5.25	27.25	965.25
05	199.25	39.25	483.25	285.25
06	955.25	5.25	40.25	6.25
07	875.25	19.25	107.25	5.25
08	745.25	56.25	174.25	31.25

PFM

	A	C	G	T
01	0.14	0.175	0.019	0.666
02	0.936	0.011	0.038	0.015
03	0.978	0.009	0.006	0.007
04	0.009	0.005	0.027	0.959
05	0.198	0.039	0.48	0.283
06	0.949	0.005	0.04	0.006
07	0.869	0.019	0.107	0.005
08	0.74	0.056	0.173	0.031

PWM

	A	C	G	T
01	-0.574	-0.355	-2.504	0.976
02	1.316	-2.991	-1.853	-2.718
03	1.359	-3.162	-3.49	-3.369
04	-3.139	-3.592	-2.169	1.339
05	-0.232	-1.822	0.649	0.124
06	1.329	-3.592	-1.798	-3.459
07	1.241	-2.492	-0.844	-3.592
08	1.081	-1.475	-0.365	-2.039

Standard thresholds

P-value	Threshold
0.001	4.724845
0.0005	5.63559
0.0001	7.3974