LMX1A.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LMX1A.H12INVIVO.0.SM.D
Gene (human)	LMX1A (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lmx1a
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	12
Consensus	nnnYTAATTRnn
GC content	24.34%
Information content (bits; total / per base)	11.496 / 0.958
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9172

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.959	0.931	0.9	0.873	0.764	0.765
Overall, 4 experiments	best	0.979	0.961	0.97	0.95	0.919	0.898
Methyl HT-SELEX, 1 experiments	median	0.952	0.917	0.909	0.874	0.821	0.795
Methyl HT-SELEX, 1 experiments	best	0.952	0.917	0.909	0.874	0.821	0.795
Non-Methyl HT-SELEX, 3 experiments	median	0.966	0.945	0.89	0.872	0.707	0.735
Non-Methyl HT-SELEX, 3 experiments	best	0.979	0.961	0.97	0.95	0.919	0.898

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.971	0.925	0.899	0.635

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: 3.1.5.6.1
HGNC	HGNC:6653
MGI	MGI:1888519
EntrezGene (human)	GeneID:4009 (SSTAR profile)
EntrezGene (mouse)	GeneID:110648 (SSTAR profile)
UniProt ID (human)	LMX1A_HUMAN
UniProt ID (mouse)	LMX1A_MOUSE
UniProt AC (human)	Q8TE12 (TFClass)
UniProt AC (mouse)	Q9JKU8 (TFClass)
GRECO-DB-TF	yes

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

PCM	LMX1A.H12INVIVO.0.SM.D.pcm
PWM	LMX1A.H12INVIVO.0.SM.D.pwm
PFM	LMX1A.H12INVIVO.0.SM.D.pfm
Alignment	LMX1A.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	LMX1A.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	LMX1A.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	LMX1A.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	LMX1A.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	LMX1A.H12INVIVO.0.SM.D_homer_format_0.001.txt LMX1A.H12INVIVO.0.SM.D_homer_format_0.0005.txt LMX1A.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2078.0	2208.0	1976.0	2910.0
02	2599.5	2530.5	1802.5	2239.5
03	3197.0	2196.0	1985.0	1794.0
04	216.0	2000.0	1172.0	5784.0
05	0.0	0.0	0.0	9172.0
06	9172.0	0.0	0.0	0.0
07	9172.0	0.0	0.0	0.0
08	0.0	0.0	0.0	9172.0
09	11.0	33.0	69.0	9059.0
10	6545.0	206.0	2147.0	274.0
11	2684.75	2181.75	2612.75	1692.75
12	3006.25	1871.25	1794.25	2500.25

PFM

	A	C	G	T
01	0.227	0.241	0.215	0.317
02	0.283	0.276	0.197	0.244
03	0.349	0.239	0.216	0.196
04	0.024	0.218	0.128	0.631
05	0.0	0.0	0.0	1.0
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.001	0.004	0.008	0.988
10	0.714	0.022	0.234	0.03
11	0.293	0.238	0.285	0.185
12	0.328	0.204	0.196	0.273

PWM

	A	C	G	T
01	-0.098	-0.038	-0.149	0.238
02	0.125	0.098	-0.24	-0.024
03	0.332	-0.043	-0.144	-0.245
04	-2.353	-0.137	-0.67	0.925
05	-6.914	-6.914	-6.914	1.386
06	1.386	-6.914	-6.914	-6.914
07	1.386	-6.914	-6.914	-6.914
08	-6.914	-6.914	-6.914	1.386
09	-5.152	-4.175	-3.472	1.373
10	1.048	-2.4	-0.066	-2.117
11	0.158	-0.05	0.13	-0.303
12	0.271	-0.203	-0.245	0.086

Standard thresholds

P-value	Threshold
0.001	3.090715
0.0005	5.25331
0.0001	7.93318