NPAS2.H14INVITRO.1.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NPAS2.H14INVITRO.1.M.C
Gene (human)	NPAS2 (GeneCards)
Gene synonyms (human)	BHLHE9, MOP4, PASD4
Gene (mouse)	Npas2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	C

Motif length	11
Consensus	nvRCATGYGKn
GC content	52.2%
Information content (bits; total / per base)	10.97 / 0.997
Data sources	Methyl-HT-SELEX
Aligned words	9635
Previous names	NPAS2.H12INVITRO.1.M.C

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.948	0.91	0.908	0.879	0.825	0.812
Overall, 4 experiments	best	0.982	0.97	0.974	0.955	0.976	0.954
Methyl HT-SELEX, 2 experiments	median	0.856	0.839	0.8	0.789	0.758	0.748
Methyl HT-SELEX, 2 experiments	best	0.982	0.97	0.972	0.955	0.939	0.919
Non-Methyl HT-SELEX, 2 experiments	median	0.948	0.91	0.909	0.879	0.843	0.83
Non-Methyl HT-SELEX, 2 experiments	best	0.975	0.957	0.974	0.953	0.976	0.954

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.795	0.609	0.405	0.226

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	NPAS2.H14INVITRO.1.M.C.pcm
PWM	NPAS2.H14INVITRO.1.M.C.pwm
PFM	NPAS2.H14INVITRO.1.M.C.pfm
Threshold to P-value map	NPAS2.H14INVITRO.1.M.C.thr
Motif in other formats
JASPAR format	NPAS2.H14INVITRO.1.M.C_jaspar_format.txt
MEME format	NPAS2.H14INVITRO.1.M.C_meme_format.meme
Transfac format	NPAS2.H14INVITRO.1.M.C_transfac_format.txt
Homer format	NPAS2.H14INVITRO.1.M.C_homer_format_0.001.txt NPAS2.H14INVITRO.1.M.C_homer_format_0.0005.txt NPAS2.H14INVITRO.1.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2984.75	1564.75	2910.75	2174.75
02	3915.75	1667.75	2594.75	1456.75
03	5830.0	746.0	3047.0	12.0
04	26.0	9464.0	122.0	23.0
05	9258.0	3.0	369.0	5.0
06	1.0	997.0	29.0	8608.0
07	72.0	0.0	9560.0	3.0
08	44.0	3967.0	66.0	5558.0
09	33.0	90.0	9151.0	361.0
10	192.75	1978.75	2283.75	5179.75
11	2299.5	2753.5	1959.5	2622.5

PFM

	A	C	G	T
01	0.31	0.162	0.302	0.226
02	0.406	0.173	0.269	0.151
03	0.605	0.077	0.316	0.001
04	0.003	0.982	0.013	0.002
05	0.961	0.0	0.038	0.001
06	0.0	0.103	0.003	0.893
07	0.007	0.0	0.992	0.0
08	0.005	0.412	0.007	0.577
09	0.003	0.009	0.95	0.037
10	0.02	0.205	0.237	0.538
11	0.239	0.286	0.203	0.272

PWM

	A	C	G	T
01	0.214	-0.431	0.189	-0.102
02	0.486	-0.367	0.074	-0.502
03	0.883	-1.17	0.235	-5.128
04	-4.445	1.368	-2.965	-4.557
05	1.346	-6.121	-1.871	-5.801
06	-6.596	-0.881	-4.344	1.273
07	-3.48	-6.958	1.378	-6.121
08	-3.953	0.499	-3.564	0.836
09	-4.224	-3.263	1.334	-1.893
10	-2.515	-0.196	-0.053	0.765
11	-0.046	0.134	-0.206	0.085

Standard thresholds

P-value	Threshold
0.001	4.165535
0.0005	5.397125
0.0001	7.867005