NPAS2.H12INVIVO.2.S.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NPAS2.H12INVIVO.2.S.D
Gene (human)	NPAS2 (GeneCards)
Gene synonyms (human)	BHLHE9, MOP4, PASD4
Gene (mouse)	Npas2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	D

Motif length	21
Consensus	vCACGTGbnnnMCACGTGYhn
GC content	57.88%
Information content (bits; total / per base)	21.092 / 1.004
Data sources	HT-SELEX
Aligned words	8715

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.981	0.972	0.898	0.887	0.784	0.783
Overall, 4 experiments	best	1.0	1.0	0.999	0.998	0.994	0.992
Methyl HT-SELEX, 2 experiments	median	0.831	0.814	0.766	0.75	0.706	0.694
Methyl HT-SELEX, 2 experiments	best	0.969	0.952	0.922	0.897	0.848	0.823
Non-Methyl HT-SELEX, 2 experiments	median	0.997	0.996	0.936	0.937	0.857	0.867
Non-Methyl HT-SELEX, 2 experiments	best	1.0	1.0	0.999	0.998	0.994	0.992

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.817	0.756	0.809	0.576

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.2.S.D.pcm
PWM	NPAS2.H12INVIVO.2.S.D.pwm
PFM	NPAS2.H12INVIVO.2.S.D.pfm
Alignment	NPAS2.H12INVIVO.2.S.D.words.tsv
Threshold to P-value map	NPAS2.H12INVIVO.2.S.D.thr
Motif in other formats
JASPAR format	NPAS2.H12INVIVO.2.S.D_jaspar_format.txt
MEME format	NPAS2.H12INVIVO.2.S.D_meme_format.meme
Transfac format	NPAS2.H12INVIVO.2.S.D_transfac_format.txt
Homer format	NPAS2.H12INVIVO.2.S.D_homer_format_0.001.txt NPAS2.H12INVIVO.2.S.D_homer_format_0.0005.txt NPAS2.H12INVIVO.2.S.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2698.0	2051.0	3062.0	904.0
02	731.5	7640.5	145.5	197.5
03	7191.0	244.0	1040.0	240.0
04	151.0	7589.0	268.0	707.0
05	615.0	216.0	7657.0	227.0
06	153.0	826.0	357.0	7379.0
07	148.0	171.0	7818.0	578.0
08	625.0	2950.0	2075.0	3065.0
09	2728.0	2051.0	1475.0	2461.0
10	2827.0	1457.0	1802.0	2629.0
11	2639.0	1230.0	2760.0	2086.0
12	4685.0	2052.0	1859.0	119.0
13	0.0	8715.0	0.0	0.0
14	8714.0	0.0	1.0	0.0
15	0.0	8712.0	0.0	3.0
16	0.0	0.0	8712.0	3.0
17	0.0	5.0	2.0	8708.0
18	0.0	1.0	8700.0	14.0
19	84.0	2091.0	1858.0	4682.0
20	2534.5	3481.5	821.5	1877.5
21	2489.75	2338.75	1700.75	2185.75

PFM

	A	C	G	T
01	0.31	0.235	0.351	0.104
02	0.084	0.877	0.017	0.023
03	0.825	0.028	0.119	0.028
04	0.017	0.871	0.031	0.081
05	0.071	0.025	0.879	0.026
06	0.018	0.095	0.041	0.847
07	0.017	0.02	0.897	0.066
08	0.072	0.338	0.238	0.352
09	0.313	0.235	0.169	0.282
10	0.324	0.167	0.207	0.302
11	0.303	0.141	0.317	0.239
12	0.538	0.235	0.213	0.014
13	0.0	1.0	0.0	0.0
14	1.0	0.0	0.0	0.0
15	0.0	1.0	0.0	0.0
16	0.0	0.0	1.0	0.0
17	0.0	0.001	0.0	0.999
18	0.0	0.0	0.998	0.002
19	0.01	0.24	0.213	0.537
20	0.291	0.399	0.094	0.215
21	0.286	0.268	0.195	0.251

PWM

	A	C	G	T
01	0.214	-0.06	0.34	-0.878
02	-1.089	1.254	-2.692	-2.39
03	1.193	-2.181	-0.738	-2.198
04	-2.655	1.247	-2.088	-1.123
05	-1.262	-2.302	1.256	-2.253
06	-2.642	-0.968	-1.803	1.219
07	-2.675	-2.533	1.277	-1.324
08	-1.246	0.303	-0.049	0.341
09	0.225	-0.06	-0.39	0.122
10	0.26	-0.402	-0.19	0.188
11	0.191	-0.571	0.236	-0.043
12	0.765	-0.06	-0.159	-2.89
13	-6.869	1.386	-6.869	-6.869
14	1.385	-6.869	-6.503	-6.869
15	-6.869	1.385	-6.869	-6.026
16	-6.869	-6.869	1.385	-6.026
17	-6.869	-5.704	-6.236	1.385
18	-6.869	-6.503	1.384	-4.898
19	-3.23	-0.041	-0.159	0.764
20	0.151	0.468	-0.974	-0.149
21	0.133	0.071	-0.247	0.003

Standard thresholds

P-value	Threshold
0.001	-3.86804
0.0005	-1.82799
0.0001	2.43501