ALX3.H12RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	ALX3.H12RSNP.0.SM.B
Gene (human)	ALX3 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Alx3
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	15
Consensus	nvbTAATTARdKKRn
GC content	27.84%
Information content (bits; total / per base)	13.741 / 0.916
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	1590

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.961	0.932	0.949	0.916	0.909	0.876
Overall, 8 experiments	best	0.98	0.964	0.975	0.957	0.953	0.932
Methyl HT-SELEX, 2 experiments	median	0.95	0.914	0.935	0.896	0.898	0.859
Methyl HT-SELEX, 2 experiments	best	0.961	0.932	0.947	0.915	0.912	0.877
Non-Methyl HT-SELEX, 6 experiments	median	0.963	0.935	0.951	0.919	0.914	0.881
Non-Methyl HT-SELEX, 6 experiments	best	0.98	0.964	0.975	0.957	0.953	0.932

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.994	0.35	0.971	0.486
batch 2	0.799	0.628	0.787	0.567

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	Paired-related HD {3.1.3} (TFClass)
TF subfamily	ALX {3.1.3.1} (TFClass)
TFClass ID	TFClass: 3.1.3.1.2
HGNC	HGNC:449
MGI	MGI:1277097
EntrezGene (human)	GeneID:257 (SSTAR profile)
EntrezGene (mouse)	GeneID:11694 (SSTAR profile)
UniProt ID (human)	ALX3_HUMAN
UniProt ID (mouse)	ALX3_MOUSE
UniProt AC (human)	O95076 (TFClass)
UniProt AC (mouse)	O70137 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	6
Methyl-HT-SELEX	2

PCM	ALX3.H12RSNP.0.SM.B.pcm
PWM	ALX3.H12RSNP.0.SM.B.pwm
PFM	ALX3.H12RSNP.0.SM.B.pfm
Alignment	ALX3.H12RSNP.0.SM.B.words.tsv
Threshold to P-value map	ALX3.H12RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	ALX3.H12RSNP.0.SM.B_jaspar_format.txt
MEME format	ALX3.H12RSNP.0.SM.B_meme_format.meme
Transfac format	ALX3.H12RSNP.0.SM.B_transfac_format.txt
Homer format	ALX3.H12RSNP.0.SM.B_homer_format_0.001.txt ALX3.H12RSNP.0.SM.B_homer_format_0.0005.txt ALX3.H12RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	316.0	519.0	433.0	322.0
02	308.75	490.75	581.75	208.75
03	211.0	613.0	356.0	410.0
04	29.0	49.0	12.0	1500.0
05	1581.0	2.0	7.0	0.0
06	1590.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1590.0
08	0.0	22.0	2.0	1566.0
09	1403.0	28.0	156.0	3.0
10	721.0	145.0	704.0	20.0
11	875.0	162.0	319.0	234.0
12	55.0	153.0	160.0	1222.0
13	149.0	226.0	229.0	986.0
14	993.75	197.75	239.75	158.75
15	422.0	382.0	451.0	335.0

PFM

	A	C	G	T
01	0.199	0.326	0.272	0.203
02	0.194	0.309	0.366	0.131
03	0.133	0.386	0.224	0.258
04	0.018	0.031	0.008	0.943
05	0.994	0.001	0.004	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.014	0.001	0.985
09	0.882	0.018	0.098	0.002
10	0.453	0.091	0.443	0.013
11	0.55	0.102	0.201	0.147
12	0.035	0.096	0.101	0.769
13	0.094	0.142	0.144	0.62
14	0.625	0.124	0.151	0.1
15	0.265	0.24	0.284	0.211

PWM

	A	C	G	T
01	-0.228	0.266	0.085	-0.21
02	-0.251	0.21	0.379	-0.64
03	-0.629	0.432	-0.11	0.031
04	-2.561	-2.061	-3.362	1.325
05	1.377	-4.644	-3.81	-5.378
06	1.383	-5.378	-5.378	-5.378
07	-5.378	-5.378	-5.378	1.383
08	-5.378	-2.818	-4.644	1.368
09	1.258	-2.594	-0.928	-4.412
10	0.593	-1.0	0.57	-2.906
11	0.787	-0.891	-0.219	-0.527
12	-1.95	-0.947	-0.903	1.12
13	-0.974	-0.561	-0.548	0.906
14	0.914	-0.694	-0.503	-0.911
15	0.06	-0.04	0.126	-0.17

Standard thresholds

P-value	Threshold
0.001	2.99551
0.0005	4.31226
0.0001	7.01441