ALX3.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	ALX3.H12INVIVO.0.SM.D
Gene (human)	ALX3 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Alx3
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	12
Consensus	nvvYTAATTRvn
GC content	34.9%
Information content (bits; total / per base)	11.666 / 0.972
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8444

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.972	0.953	0.955	0.931	0.922	0.893
Overall, 8 experiments	best	0.997	0.995	0.992	0.988	0.977	0.97
Methyl HT-SELEX, 2 experiments	median	0.959	0.932	0.939	0.907	0.902	0.866
Methyl HT-SELEX, 2 experiments	best	0.971	0.952	0.952	0.927	0.917	0.887
Non-Methyl HT-SELEX, 6 experiments	median	0.973	0.955	0.96	0.937	0.933	0.907
Non-Methyl HT-SELEX, 6 experiments	best	0.997	0.995	0.992	0.988	0.977	0.97

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.994	0.456	0.963	0.469
batch 2	0.786	0.62	0.764	0.503

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.H12INVIVO.0.SM.D.pcm
PWM	ALX3.H12INVIVO.0.SM.D.pwm
PFM	ALX3.H12INVIVO.0.SM.D.pfm
Alignment	ALX3.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	ALX3.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	ALX3.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	ALX3.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	ALX3.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	ALX3.H12INVIVO.0.SM.D_homer_format_0.001.txt ALX3.H12INVIVO.0.SM.D_homer_format_0.0005.txt ALX3.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2344.25	1988.25	2192.25	1919.25
02	1975.5	3550.5	1745.5	1172.5
03	1816.0	2557.0	3788.0	283.0
04	196.0	3934.0	1038.0	3276.0
05	0.0	0.0	0.0	8444.0
06	8444.0	0.0	0.0	0.0
07	8444.0	0.0	0.0	0.0
08	0.0	0.0	0.0	8444.0
09	3.0	142.0	109.0	8190.0
10	5128.0	233.0	2954.0	129.0
11	1254.25	2729.25	3453.25	1007.25
12	1656.5	2328.5	2620.5	1838.5

PFM

	A	C	G	T
01	0.278	0.235	0.26	0.227
02	0.234	0.42	0.207	0.139
03	0.215	0.303	0.449	0.034
04	0.023	0.466	0.123	0.388
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	0.0	0.017	0.013	0.97
10	0.607	0.028	0.35	0.015
11	0.149	0.323	0.409	0.119
12	0.196	0.276	0.31	0.218

PWM

	A	C	G	T
01	0.105	-0.06	0.038	-0.095
02	-0.066	0.519	-0.19	-0.587
03	-0.15	0.191	0.584	-2.003
04	-2.366	0.622	-0.709	0.439
05	-6.84	-6.84	-6.84	1.385
06	1.385	-6.84	-6.84	-6.84
07	1.385	-6.84	-6.84	-6.84
08	-6.84	-6.84	-6.84	1.385
09	-5.996	-2.684	-2.944	1.355
10	0.887	-2.195	0.336	-2.779
11	-0.52	0.257	0.492	-0.739
12	-0.242	0.098	0.216	-0.138

Standard thresholds

P-value	Threshold
0.001	3.421365
0.0005	5.013625
0.0001	7.98652