ALX1.H12RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	ALX1.H12RSNP.0.SM.B
Gene (human)	ALX1 (GeneCards)
Gene synonyms (human)	CART1
Gene (mouse)	Alx1
Gene synonyms (mouse)	Cart1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	18
Consensus	nnhTAATTAGATTAdhbn
GC content	21.23%
Information content (bits; total / per base)	21.344 / 1.186
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	432

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.995	0.992	0.904	0.912	0.801	0.818
Overall, 4 experiments	best	1.0	0.999	0.993	0.989	0.973	0.967
Methyl HT-SELEX, 1 experiments	median	1.0	0.999	0.798	0.842	0.6	0.681
Methyl HT-SELEX, 1 experiments	best	1.0	0.999	0.798	0.842	0.6	0.681
Non-Methyl HT-SELEX, 3 experiments	median	0.994	0.99	0.988	0.982	0.945	0.937
Non-Methyl HT-SELEX, 3 experiments	best	0.996	0.993	0.993	0.989	0.973	0.967

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.835	0.429	0.728	0.498
batch 2	0.857	0.754	0.806	0.542

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: 3.1.3.1.1
HGNC	HGNC:1494
MGI	MGI:104621
EntrezGene (human)	GeneID:8092 (SSTAR profile)
EntrezGene (mouse)	GeneID:216285 (SSTAR profile)
UniProt ID (human)	ALX1_HUMAN
UniProt ID (mouse)	ALX1_MOUSE
UniProt AC (human)	Q15699 (TFClass)
UniProt AC (mouse)	Q8C8B0 (TFClass)
GRECO-DB-TF	yes

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

PCM	ALX1.H12RSNP.0.SM.B.pcm
PWM	ALX1.H12RSNP.0.SM.B.pwm
PFM	ALX1.H12RSNP.0.SM.B.pfm
Alignment	ALX1.H12RSNP.0.SM.B.words.tsv
Threshold to P-value map	ALX1.H12RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	ALX1.H12RSNP.0.SM.B_jaspar_format.txt
MEME format	ALX1.H12RSNP.0.SM.B_meme_format.meme
Transfac format	ALX1.H12RSNP.0.SM.B_transfac_format.txt
Homer format	ALX1.H12RSNP.0.SM.B_homer_format_0.001.txt ALX1.H12RSNP.0.SM.B_homer_format_0.0005.txt ALX1.H12RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	150.75	115.75	94.75	70.75
02	160.75	77.75	121.75	71.75
03	50.0	149.0	32.0	201.0
04	4.0	0.0	1.0	427.0
05	431.0	0.0	1.0	0.0
06	432.0	0.0	0.0	0.0
07	0.0	0.0	0.0	432.0
08	0.0	0.0	1.0	431.0
09	417.0	14.0	0.0	1.0
10	123.0	1.0	308.0	0.0
11	428.0	0.0	1.0	3.0
12	0.0	0.0	0.0	432.0
13	1.0	1.0	3.0	427.0
14	418.0	0.0	3.0	11.0
15	220.0	37.0	132.0	43.0
16	83.0	97.0	67.0	185.0
17	65.0	85.0	103.0	179.0
18	107.5	103.5	101.5	119.5

PFM

	A	C	G	T
01	0.349	0.268	0.219	0.164
02	0.372	0.18	0.282	0.166
03	0.116	0.345	0.074	0.465
04	0.009	0.0	0.002	0.988
05	0.998	0.0	0.002	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	0.002	0.998
09	0.965	0.032	0.0	0.002
10	0.285	0.002	0.713	0.0
11	0.991	0.0	0.002	0.007
12	0.0	0.0	0.0	1.0
13	0.002	0.002	0.007	0.988
14	0.968	0.0	0.007	0.025
15	0.509	0.086	0.306	0.1
16	0.192	0.225	0.155	0.428
17	0.15	0.197	0.238	0.414
18	0.249	0.24	0.235	0.277

PWM

	A	C	G	T
01	0.33	0.068	-0.129	-0.416
02	0.393	-0.323	0.118	-0.402
03	-0.754	0.318	-1.184	0.615
04	-2.988	-4.279	-3.773	1.364
05	1.374	-4.279	-3.773	-4.279
06	1.376	-4.279	-4.279	-4.279
07	-4.279	-4.279	-4.279	1.376
08	-4.279	-4.279	-3.773	1.374
09	1.341	-1.954	-4.279	-3.773
10	0.128	-3.773	1.039	-4.279
11	1.367	-4.279	-3.773	-3.188
12	-4.279	-4.279	-4.279	1.376
13	-3.773	-3.773	-3.188	1.364
14	1.343	-4.279	-3.188	-2.169
15	0.704	-1.045	0.198	-0.9
16	-0.259	-0.106	-0.469	0.532
17	-0.499	-0.236	-0.047	0.5
18	-0.005	-0.042	-0.061	0.1

Standard thresholds

P-value	Threshold
0.001	-1.90054
0.0005	-0.43739
0.0001	3.43381