NPAS2.H12INVITRO.0.M.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NPAS2.H12INVITRO.0.M.B
Gene (human)	NPAS2 (GeneCards)
Gene synonyms (human)	BHLHE9, MOP4, PASD4
Gene (mouse)	Npas2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	21
Consensus	nvCRYRYGbhWMRCAYRTGbn
GC content	48.15%
Information content (bits; total / per base)	15.714 / 0.748
Data sources	Methyl-HT-SELEX
Aligned words	6248

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.988	0.986	0.903	0.9	0.798	0.8
Overall, 4 experiments	best	0.999	0.999	0.997	0.995	0.979	0.975
Methyl HT-SELEX, 2 experiments	median	0.858	0.859	0.792	0.791	0.729	0.728
Methyl HT-SELEX, 2 experiments	best	0.993	0.991	0.965	0.956	0.891	0.879
Non-Methyl HT-SELEX, 2 experiments	median	0.991	0.99	0.919	0.919	0.842	0.848
Non-Methyl HT-SELEX, 2 experiments	best	0.999	0.999	0.997	0.995	0.979	0.975

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.556	0.411	0.634	0.444

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.H12INVITRO.0.M.B.pcm
PWM	NPAS2.H12INVITRO.0.M.B.pwm
PFM	NPAS2.H12INVITRO.0.M.B.pfm
Alignment	NPAS2.H12INVITRO.0.M.B.words.tsv
Threshold to P-value map	NPAS2.H12INVITRO.0.M.B.thr
Motif in other formats
JASPAR format	NPAS2.H12INVITRO.0.M.B_jaspar_format.txt
MEME format	NPAS2.H12INVITRO.0.M.B_meme_format.meme
Transfac format	NPAS2.H12INVITRO.0.M.B_transfac_format.txt
Homer format	NPAS2.H12INVITRO.0.M.B_homer_format_0.001.txt NPAS2.H12INVITRO.0.M.B_homer_format_0.0005.txt NPAS2.H12INVITRO.0.M.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1853.25	1292.25	1747.25	1355.25
02	3267.75	1370.75	1074.75	534.75
03	226.0	5798.0	86.0	138.0
04	4315.0	191.0	1491.0	251.0
05	320.0	2205.0	220.0	3503.0
06	1805.0	533.0	3433.0	477.0
07	146.0	1567.0	940.0	3595.0
08	194.0	224.0	5394.0	436.0
09	526.0	1617.0	1569.0	2536.0
10	3480.0	1156.0	670.0	942.0
11	4285.0	652.0	435.0	876.0
12	4013.0	968.0	790.0	477.0
13	4586.0	621.0	912.0	129.0
14	39.0	5924.0	14.0	271.0
15	5506.0	13.0	435.0	294.0
16	2.0	3363.0	6.0	2877.0
17	2849.0	330.0	3059.0	10.0
18	41.0	1845.0	10.0	4352.0
19	102.0	53.0	6011.0	82.0
20	473.5	1538.5	866.5	3369.5
21	1615.75	1760.75	989.75	1881.75

PFM

	A	C	G	T
01	0.297	0.207	0.28	0.217
02	0.523	0.219	0.172	0.086
03	0.036	0.928	0.014	0.022
04	0.691	0.031	0.239	0.04
05	0.051	0.353	0.035	0.561
06	0.289	0.085	0.549	0.076
07	0.023	0.251	0.15	0.575
08	0.031	0.036	0.863	0.07
09	0.084	0.259	0.251	0.406
10	0.557	0.185	0.107	0.151
11	0.686	0.104	0.07	0.14
12	0.642	0.155	0.126	0.076
13	0.734	0.099	0.146	0.021
14	0.006	0.948	0.002	0.043
15	0.881	0.002	0.07	0.047
16	0.0	0.538	0.001	0.46
17	0.456	0.053	0.49	0.002
18	0.007	0.295	0.002	0.697
19	0.016	0.008	0.962	0.013
20	0.076	0.246	0.139	0.539
21	0.259	0.282	0.158	0.301

PWM

	A	C	G	T
01	0.171	-0.189	0.112	-0.142
02	0.737	-0.13	-0.373	-1.069
03	-1.925	1.311	-2.876	-2.412
04	1.015	-2.091	-0.046	-1.821
05	-1.58	0.344	-1.952	0.807
06	0.144	-1.073	0.787	-1.183
07	-2.357	0.003	-0.507	0.833
08	-2.076	-1.934	1.238	-1.272
09	-1.086	0.035	0.004	0.484
10	0.8	-0.301	-0.845	-0.505
11	1.008	-0.872	-1.275	-0.577
12	0.943	-0.478	-0.68	-1.183
13	1.076	-0.92	-0.537	-2.479
14	-3.637	1.332	-4.571	-1.745
15	1.259	-4.635	-1.275	-1.664
16	-5.924	0.766	-5.253	0.61
17	0.6	-1.549	0.671	-4.855
18	-3.59	0.166	-4.855	1.024
19	-2.709	-3.344	1.347	-2.922
20	-1.19	-0.015	-0.588	0.768
21	0.034	0.12	-0.455	0.186

Standard thresholds

P-value	Threshold
0.001	2.70321
0.0005	3.89541
0.0001	6.37536