NPAS2.H12INVIVO.1.M.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NPAS2.H12INVIVO.1.M.D
Gene (human)	NPAS2 (GeneCards)
Gene synonyms (human)	BHLHE9, MOP4, PASD4
Gene (mouse)	Npas2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	11
Consensus	nvRCATGTGKn
GC content	50.71%
Information content (bits; total / per base)	12.177 / 1.107
Data sources	Methyl-HT-SELEX
Aligned words	7767

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.936	0.893	0.905	0.868	0.825	0.809
Overall, 4 experiments	best	0.982	0.97	0.971	0.954	0.971	0.944
Methyl HT-SELEX, 2 experiments	median	0.857	0.838	0.8	0.788	0.758	0.748
Methyl HT-SELEX, 2 experiments	best	0.982	0.97	0.971	0.954	0.939	0.918
Non-Methyl HT-SELEX, 2 experiments	median	0.936	0.893	0.905	0.868	0.841	0.822
Non-Methyl HT-SELEX, 2 experiments	best	0.969	0.95	0.967	0.941	0.971	0.944

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.818	0.632	0.393	0.235

TF superclass	Basic domains {1} (TFClass)
TF class	Basic helix-loop-helix factors (bHLH) {1.2} (TFClass)
TF family	PAS {1.2.5} (TFClass)
TF subfamily	PAS-ARNT {1.2.5.2} (TFClass)
TFClass ID	TFClass: 1.2.5.2.6
HGNC	HGNC:7895
MGI	MGI:109232
EntrezGene (human)	GeneID:4862 (SSTAR profile)
EntrezGene (mouse)	GeneID:18143 (SSTAR profile)
UniProt ID (human)	NPAS2_HUMAN
UniProt ID (mouse)	NPAS2_MOUSE
UniProt AC (human)	Q99743 (TFClass)
UniProt AC (mouse)	P97460 (TFClass)
GRECO-DB-TF	yes

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

PCM	NPAS2.H12INVIVO.1.M.D.pcm
PWM	NPAS2.H12INVIVO.1.M.D.pwm
PFM	NPAS2.H12INVIVO.1.M.D.pfm
Alignment	NPAS2.H12INVIVO.1.M.D.words.tsv
Threshold to P-value map	NPAS2.H12INVIVO.1.M.D.thr
Motif in other formats
JASPAR format	NPAS2.H12INVIVO.1.M.D_jaspar_format.txt
MEME format	NPAS2.H12INVIVO.1.M.D_meme_format.meme
Transfac format	NPAS2.H12INVIVO.1.M.D_transfac_format.txt
Homer format	NPAS2.H12INVIVO.1.M.D_homer_format_0.001.txt NPAS2.H12INVIVO.1.M.D_homer_format_0.0005.txt NPAS2.H12INVIVO.1.M.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2474.25	1221.25	2341.25	1730.25
02	3382.0	1376.0	1940.0	1069.0
03	5061.0	436.0	2266.0	4.0
04	0.0	7766.0	1.0	0.0
05	7743.0	0.0	24.0	0.0
06	0.0	307.0	0.0	7460.0
07	15.0	0.0	7752.0	0.0
08	5.0	3168.0	2.0	4592.0
09	1.0	9.0	7677.0	80.0
10	100.5	1474.5	1840.5	4351.5
11	1871.25	2234.25	1485.25	2176.25

PFM

	A	C	G	T
01	0.319	0.157	0.301	0.223
02	0.435	0.177	0.25	0.138
03	0.652	0.056	0.292	0.001
04	0.0	1.0	0.0	0.0
05	0.997	0.0	0.003	0.0
06	0.0	0.04	0.0	0.96
07	0.002	0.0	0.998	0.0
08	0.001	0.408	0.0	0.591
09	0.0	0.001	0.988	0.01
10	0.013	0.19	0.237	0.56
11	0.241	0.288	0.191	0.28

PWM

	A	C	G	T
01	0.242	-0.463	0.187	-0.115
02	0.554	-0.344	-0.001	-0.596
03	0.957	-1.49	0.154	-5.742
04	-6.766	1.385	-6.397	-6.766
05	1.382	-6.766	-4.305	-6.766
06	-6.766	-1.838	-6.766	1.345
07	-4.725	-6.766	1.383	-6.766
08	-5.593	0.489	-6.128	0.86
09	-6.397	-5.153	1.374	-3.163
10	-2.94	-0.275	-0.053	0.806
11	-0.037	0.14	-0.268	0.114

Standard thresholds

P-value	Threshold
0.001	2.50998
0.0005	4.339065
0.0001	7.996815