ARX.H13INVIVO.1.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	ARX.H13INVIVO.1.SM.D
Gene (human)	ARX (GeneCards)
Gene synonyms (human)
Gene (mouse)	Arx
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	12
Consensus	nnYRATTARbbn
GC content	35.72%
Information content (bits; total / per base)	10.658 / 0.888
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8668
Previous names	ARX.H12INVIVO.1.SM.D

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.981	0.967	0.974	0.956	0.956	0.934
Overall, 6 experiments	best	0.988	0.981	0.985	0.974	0.975	0.962
Methyl HT-SELEX, 1 experiments	median	0.962	0.936	0.948	0.917	0.925	0.889
Methyl HT-SELEX, 1 experiments	best	0.962	0.936	0.948	0.917	0.925	0.889
Non-Methyl HT-SELEX, 5 experiments	median	0.985	0.975	0.978	0.964	0.956	0.937
Non-Methyl HT-SELEX, 5 experiments	best	0.988	0.981	0.985	0.974	0.975	0.962

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.75	0.516	0.74	0.521

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	ARX {3.1.3.3} (TFClass)
TFClass ID	TFClass: 3.1.3.3.1
HGNC	HGNC:18060
MGI	MGI:1097716
EntrezGene (human)	GeneID:170302 (SSTAR profile)
EntrezGene (mouse)	GeneID:11878 (SSTAR profile)
UniProt ID (human)	ARX_HUMAN
UniProt ID (mouse)	ARX_MOUSE
UniProt AC (human)	Q96QS3 (TFClass)
UniProt AC (mouse)	O35085 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	5
Methyl-HT-SELEX	1
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	ARX.H13INVIVO.1.SM.D.pcm
PWM	ARX.H13INVIVO.1.SM.D.pwm
PFM	ARX.H13INVIVO.1.SM.D.pfm
Threshold to P-value map	ARX.H13INVIVO.1.SM.D.thr
Motif in other formats
JASPAR format	ARX.H13INVIVO.1.SM.D_jaspar_format.txt
MEME format	ARX.H13INVIVO.1.SM.D_meme_format.meme
Transfac format	ARX.H13INVIVO.1.SM.D_transfac_format.txt
Homer format	ARX.H13INVIVO.1.SM.D_homer_format_0.001.txt ARX.H13INVIVO.1.SM.D_homer_format_0.0005.txt ARX.H13INVIVO.1.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2122.25	2363.25	2172.25	2010.25
02	1024.0	2697.0	2570.0	2377.0
03	410.0	3008.0	548.0	4702.0
04	6430.0	480.0	1727.0	31.0
05	8668.0	0.0	0.0	0.0
06	0.0	0.0	0.0	8668.0
07	0.0	0.0	0.0	8668.0
08	8668.0	0.0	0.0	0.0
09	2234.0	681.0	5725.0	28.0
10	628.0	3266.0	2602.0	2172.0
11	987.25	1884.25	3357.25	2439.25
12	2013.0	2132.0	1939.0	2584.0

PFM

	A	C	G	T
01	0.245	0.273	0.251	0.232
02	0.118	0.311	0.296	0.274
03	0.047	0.347	0.063	0.542
04	0.742	0.055	0.199	0.004
05	1.0	0.0	0.0	0.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	0.0	1.0
08	1.0	0.0	0.0	0.0
09	0.258	0.079	0.66	0.003
10	0.072	0.377	0.3	0.251
11	0.114	0.217	0.387	0.281
12	0.232	0.246	0.224	0.298

PWM

	A	C	G	T
01	-0.021	0.087	0.002	-0.075
02	-0.748	0.219	0.17	0.092
03	-1.66	0.328	-1.372	0.774
04	1.087	-1.504	-0.227	-4.178
05	1.386	-6.864	-6.864	-6.864
06	-6.864	-6.864	-6.864	1.386
07	-6.864	-6.864	-6.864	1.386
08	1.386	-6.864	-6.864	-6.864
09	0.03	-1.155	0.971	-4.272
10	-1.236	0.41	0.183	0.002
11	-0.785	-0.14	0.437	0.118
12	-0.074	-0.016	-0.111	0.176

Standard thresholds

P-value	Threshold
0.001	4.709215
0.0005	5.978815
0.0001	7.743005