LMX1B.H12INVITRO.2.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LMX1B.H12INVITRO.2.S.B
Gene (human)	LMX1B (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lmx1b
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	18
Consensus	vvYTAATTAATYRhWWWh
GC content	18.97%
Information content (bits; total / per base)	18.708 / 1.039
Data sources	HT-SELEX
Aligned words	635

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)	0.667	0.694	0.511	0.585	0.609	0.619	1.581	1.619	22.886	34.131

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.978	0.963	0.961	0.942	0.877	0.868
Overall, 8 experiments	best	0.991	0.983	0.989	0.98	0.982	0.969
Methyl HT-SELEX, 2 experiments	median	0.988	0.98	0.984	0.973	0.953	0.941
Methyl HT-SELEX, 2 experiments	best	0.991	0.983	0.989	0.98	0.976	0.966
Non-Methyl HT-SELEX, 6 experiments	median	0.965	0.943	0.931	0.904	0.803	0.8
Non-Methyl HT-SELEX, 6 experiments	best	0.989	0.98	0.987	0.975	0.982	0.969

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.949	0.633	0.899	0.51
batch 2	0.758	0.552	0.75	0.538

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

PCM	LMX1B.H12INVITRO.2.S.B.pcm
PWM	LMX1B.H12INVITRO.2.S.B.pwm
PFM	LMX1B.H12INVITRO.2.S.B.pfm
Alignment	LMX1B.H12INVITRO.2.S.B.words.tsv
Threshold to P-value map	LMX1B.H12INVITRO.2.S.B.thr
Motif in other formats
JASPAR format	LMX1B.H12INVITRO.2.S.B_jaspar_format.txt
MEME format	LMX1B.H12INVITRO.2.S.B_meme_format.meme
Transfac format	LMX1B.H12INVITRO.2.S.B_transfac_format.txt
Homer format	LMX1B.H12INVITRO.2.S.B_homer_format_0.001.txt LMX1B.H12INVITRO.2.S.B_homer_format_0.0005.txt LMX1B.H12INVITRO.2.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	166.5	255.5	110.5	102.5
02	196.75	268.75	98.75	70.75
03	12.0	295.0	93.0	235.0
04	0.0	10.0	2.0	623.0
05	635.0	0.0	0.0	0.0
06	635.0	0.0	0.0	0.0
07	0.0	0.0	0.0	635.0
08	0.0	0.0	0.0	635.0
09	635.0	0.0	0.0	0.0
10	517.0	19.0	99.0	0.0
11	2.0	49.0	56.0	528.0
12	77.0	81.0	35.0	442.0
13	485.0	40.0	70.0	40.0
14	331.0	79.0	70.0	155.0
15	79.0	51.0	22.0	483.0
16	233.0	35.0	32.0	335.0
17	377.0	46.0	68.0	144.0
18	251.0	93.0	90.0	201.0

PFM

	A	C	G	T
01	0.262	0.402	0.174	0.161
02	0.31	0.423	0.156	0.111
03	0.019	0.465	0.146	0.37
04	0.0	0.016	0.003	0.981
05	1.0	0.0	0.0	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	1.0	0.0	0.0	0.0
10	0.814	0.03	0.156	0.0
11	0.003	0.077	0.088	0.831
12	0.121	0.128	0.055	0.696
13	0.764	0.063	0.11	0.063
14	0.521	0.124	0.11	0.244
15	0.124	0.08	0.035	0.761
16	0.367	0.055	0.05	0.528
17	0.594	0.072	0.107	0.227
18	0.395	0.146	0.142	0.317

PWM

	A	C	G	T
01	0.047	0.472	-0.358	-0.432
02	0.213	0.522	-0.469	-0.796
03	-2.466	0.615	-0.528	0.389
04	-4.599	-2.625	-3.793	1.36
05	1.379	-4.599	-4.599	-4.599
06	1.379	-4.599	-4.599	-4.599
07	-4.599	-4.599	-4.599	1.379
08	-4.599	-4.599	-4.599	1.379
09	1.379	-4.599	-4.599	-4.599
10	1.174	-2.052	-0.466	-4.599
11	-3.793	-1.153	-1.024	1.195
12	-0.713	-0.663	-1.477	1.018
13	1.11	-1.349	-0.806	-1.349
14	0.73	-0.688	-0.806	-0.024
15	-0.688	-1.114	-1.916	1.106
16	0.38	-1.477	-1.563	0.741
17	0.859	-1.214	-0.834	-0.096
18	0.454	-0.528	-0.56	0.234

Standard thresholds

P-value	Threshold
0.001	0.25696
0.0005	1.80586
0.0001	5.02951