NPAS2.H12INVIVO.0.M.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NPAS2.H12INVIVO.0.M.D
Gene (human)	NPAS2 (GeneCards)
Gene synonyms (human)	BHLHE9, MOP4, PASD4
Gene (mouse)	Npas2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	20
Consensus	vvRbRbRbndvACATGTGKn
GC content	51.48%
Information content (bits; total / per base)	14.55 / 0.727
Data sources	Methyl-HT-SELEX
Aligned words	379

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.982	0.977	0.911	0.903	0.818	0.816
Overall, 4 experiments	best	0.998	0.997	0.994	0.991	0.984	0.978
Methyl HT-SELEX, 2 experiments	median	0.857	0.852	0.797	0.791	0.747	0.741
Methyl HT-SELEX, 2 experiments	best	0.988	0.983	0.969	0.957	0.921	0.903
Non-Methyl HT-SELEX, 2 experiments	median	0.987	0.984	0.923	0.92	0.849	0.853
Non-Methyl HT-SELEX, 2 experiments	best	0.998	0.997	0.994	0.991	0.984	0.978

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.711	0.551	0.548	0.326

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.0.M.D.pcm
PWM	NPAS2.H12INVIVO.0.M.D.pwm
PFM	NPAS2.H12INVIVO.0.M.D.pfm
Alignment	NPAS2.H12INVIVO.0.M.D.words.tsv
Threshold to P-value map	NPAS2.H12INVIVO.0.M.D.thr
Motif in other formats
JASPAR format	NPAS2.H12INVIVO.0.M.D_jaspar_format.txt
MEME format	NPAS2.H12INVIVO.0.M.D_meme_format.meme
Transfac format	NPAS2.H12INVIVO.0.M.D_transfac_format.txt
Homer format	NPAS2.H12INVIVO.0.M.D_homer_format_0.001.txt NPAS2.H12INVIVO.0.M.D_homer_format_0.0005.txt NPAS2.H12INVIVO.0.M.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	154.75	62.75	118.75	42.75
02	69.5	209.5	75.5	24.5
03	194.0	21.0	134.0	30.0
04	39.0	101.0	76.0	163.0
05	124.0	14.0	216.0	25.0
06	37.0	80.0	93.0	169.0
07	35.0	17.0	294.0	33.0
08	45.0	49.0	145.0	140.0
09	143.0	63.0	97.0	76.0
10	190.0	17.0	110.0	62.0
11	208.0	49.0	97.0	25.0
12	284.0	19.0	76.0	0.0
13	1.0	376.0	2.0	0.0
14	357.0	0.0	22.0	0.0
15	0.0	72.0	0.0	307.0
16	48.0	0.0	331.0	0.0
17	1.0	128.0	0.0	250.0
18	2.0	0.0	374.0	3.0
19	7.0	74.0	97.0	201.0
20	77.5	103.5	88.5	109.5

PFM

	A	C	G	T
01	0.408	0.166	0.313	0.113
02	0.183	0.553	0.199	0.065
03	0.512	0.055	0.354	0.079
04	0.103	0.266	0.201	0.43
05	0.327	0.037	0.57	0.066
06	0.098	0.211	0.245	0.446
07	0.092	0.045	0.776	0.087
08	0.119	0.129	0.383	0.369
09	0.377	0.166	0.256	0.201
10	0.501	0.045	0.29	0.164
11	0.549	0.129	0.256	0.066
12	0.749	0.05	0.201	0.0
13	0.003	0.992	0.005	0.0
14	0.942	0.0	0.058	0.0
15	0.0	0.19	0.0	0.81
16	0.127	0.0	0.873	0.0
17	0.003	0.338	0.0	0.66
18	0.005	0.0	0.987	0.008
19	0.018	0.195	0.256	0.53
20	0.204	0.273	0.234	0.289

PWM

	A	C	G	T
01	0.485	-0.404	0.223	-0.777
02	-0.304	0.785	-0.223	-1.309
03	0.709	-1.454	0.342	-1.117
04	-0.866	0.063	-0.217	0.536
05	0.265	-1.827	0.815	-1.29
06	-0.917	-0.166	-0.018	0.572
07	-0.97	-1.65	1.122	-1.026
08	-0.728	-0.645	0.42	0.385
09	0.406	-0.4	0.023	-0.217
10	0.688	-1.65	0.147	-0.416
11	0.778	-0.645	0.023	-1.29
12	1.087	-1.547	-0.217	-4.172
13	-3.657	1.367	-3.318	-4.172
14	1.315	-4.172	-1.41	-4.172
15	-4.172	-0.27	-4.172	1.165
16	-0.665	-4.172	1.24	-4.172
17	-3.657	0.297	-4.172	0.961
18	-3.318	-4.172	1.361	-3.066
19	-2.429	-0.243	0.023	0.744
20	-0.198	0.087	-0.067	0.143

Standard thresholds

P-value	Threshold
0.001	3.26876
0.0005	4.44246
0.0001	6.85211