NPAS2.H12RSNP.2.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NPAS2.H12RSNP.2.S.B
Gene (human)	NPAS2 (GeneCards)
Gene synonyms (human)	BHLHE9, MOP4, PASD4
Gene (mouse)	Npas2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	22
Consensus	nvCACGTGbndRMCACGTGbhn
GC content	57.01%
Information content (bits; total / per base)	26.042 / 1.184
Data sources	HT-SELEX
Aligned words	1900

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.98	0.973	0.884	0.875	0.767	0.767
Overall, 4 experiments	best	1.0	1.0	0.998	0.997	0.982	0.978
Methyl HT-SELEX, 2 experiments	median	0.833	0.823	0.761	0.75	0.693	0.686
Methyl HT-SELEX, 2 experiments	best	0.971	0.959	0.916	0.894	0.825	0.806
Non-Methyl HT-SELEX, 2 experiments	median	0.994	0.993	0.925	0.926	0.845	0.853
Non-Methyl HT-SELEX, 2 experiments	best	1.0	1.0	0.998	0.997	0.982	0.978

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.817	0.654	0.818	0.6

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.H12RSNP.2.S.B.pcm
PWM	NPAS2.H12RSNP.2.S.B.pwm
PFM	NPAS2.H12RSNP.2.S.B.pfm
Alignment	NPAS2.H12RSNP.2.S.B.words.tsv
Threshold to P-value map	NPAS2.H12RSNP.2.S.B.thr
Motif in other formats
JASPAR format	NPAS2.H12RSNP.2.S.B_jaspar_format.txt
MEME format	NPAS2.H12RSNP.2.S.B_meme_format.meme
Transfac format	NPAS2.H12RSNP.2.S.B_transfac_format.txt
Homer format	NPAS2.H12RSNP.2.S.B_homer_format_0.001.txt NPAS2.H12RSNP.2.S.B_homer_format_0.0005.txt NPAS2.H12RSNP.2.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	477.25	346.25	556.25	520.25
02	886.0	457.0	494.0	63.0
03	9.0	1886.0	2.0	3.0
04	1869.0	4.0	25.0	2.0
05	2.0	1878.0	6.0	14.0
06	11.0	0.0	1888.0	1.0
07	0.0	9.0	1.0	1890.0
08	4.0	0.0	1887.0	9.0
09	57.0	839.0	518.0	486.0
10	694.0	339.0	430.0	437.0
11	730.0	232.0	431.0	507.0
12	831.0	37.0	773.0	259.0
13	1357.0	376.0	136.0	31.0
14	1.0	1899.0	0.0	0.0
15	1894.0	0.0	6.0	0.0
16	0.0	1900.0	0.0	0.0
17	0.0	0.0	1900.0	0.0
18	0.0	0.0	0.0	1900.0
19	0.0	0.0	1900.0	0.0
20	54.0	558.0	380.0	908.0
21	528.0	698.0	240.0	434.0
22	604.0	435.0	363.0	498.0

PFM

	A	C	G	T
01	0.251	0.182	0.293	0.274
02	0.466	0.241	0.26	0.033
03	0.005	0.993	0.001	0.002
04	0.984	0.002	0.013	0.001
05	0.001	0.988	0.003	0.007
06	0.006	0.0	0.994	0.001
07	0.0	0.005	0.001	0.995
08	0.002	0.0	0.993	0.005
09	0.03	0.442	0.273	0.256
10	0.365	0.178	0.226	0.23
11	0.384	0.122	0.227	0.267
12	0.437	0.019	0.407	0.136
13	0.714	0.198	0.072	0.016
14	0.001	0.999	0.0	0.0
15	0.997	0.0	0.003	0.0
16	0.0	1.0	0.0	0.0
17	0.0	0.0	1.0	0.0
18	0.0	0.0	0.0	1.0
19	0.0	0.0	1.0	0.0
20	0.028	0.294	0.2	0.478
21	0.278	0.367	0.126	0.228
22	0.318	0.229	0.191	0.262

PWM

	A	C	G	T
01	0.005	-0.315	0.157	0.091
02	0.622	-0.038	0.039	-1.995
03	-3.78	1.376	-4.81	-4.581
04	1.367	-4.394	-2.876	-4.81
05	-4.81	1.372	-4.102	-3.402
06	-3.611	-5.532	1.377	-5.107
07	-5.532	-3.78	-5.107	1.378
08	-4.394	-5.532	1.376	-3.78
09	-2.092	0.567	0.086	0.023
10	0.378	-0.336	-0.099	-0.083
11	0.428	-0.712	-0.097	0.065
12	0.558	-2.507	0.485	-0.603
13	1.047	-0.233	-1.241	-2.674
14	-5.107	1.383	-5.532	-5.532
15	1.38	-5.532	-4.102	-5.532
16	-5.532	1.383	-5.532	-5.532
17	-5.532	-5.532	1.383	-5.532
18	-5.532	-5.532	-5.532	1.383
19	-5.532	-5.532	1.383	-5.532
20	-2.144	0.16	-0.222	0.646
21	0.105	0.384	-0.679	-0.09
22	0.239	-0.088	-0.268	0.047

Standard thresholds

P-value	Threshold
0.001	-9.27019
0.0005	-7.12899
0.0001	-2.29849