NDF2.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NDF2.H12INVIVO.0.P.B
Gene (human)	NEUROD2 (GeneCards)
Gene synonyms (human)	BHLHA1, NDRF
Gene (mouse)	Neurod2
Gene synonyms (mouse)	Ndrf
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	11
Consensus	RRCAGMTGGbn
GC content	58.72%
Information content (bits; total / per base)	12.257 / 1.114
Data sources	ChIP-Seq
Aligned words	1000

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Mouse	8 (46)	0.913	0.962	0.831	0.915	0.868	0.927	2.954	3.412	182.4	251.377

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.646	0.604	0.588	0.568	0.555	0.546
Non-Methyl HT-SELEX, 2 experiments	best	0.652	0.609	0.59	0.57	0.556	0.547

TF superclass	Basic domains {1} (TFClass)
TF class	Basic helix-loop-helix factors (bHLH) {1.2} (TFClass)
TF family	Tal-related {1.2.3} (TFClass)
TF subfamily	Neurogenin-ATO {1.2.3.4} (TFClass)
TFClass ID	TFClass: 1.2.3.4.2
HGNC	HGNC:7763
MGI	MGI:107755
EntrezGene (human)	GeneID:4761 (SSTAR profile)
EntrezGene (mouse)	GeneID:18013 (SSTAR profile)
UniProt ID (human)	NDF2_HUMAN
UniProt ID (mouse)	NDF2_MOUSE
UniProt AC (human)	Q15784 (TFClass)
UniProt AC (mouse)	Q62414 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 8 mouse
HT-SELEX	2
Methyl-HT-SELEX	0

PCM	NDF2.H12INVIVO.0.P.B.pcm
PWM	NDF2.H12INVIVO.0.P.B.pwm
PFM	NDF2.H12INVIVO.0.P.B.pfm
Alignment	NDF2.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	NDF2.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	NDF2.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	NDF2.H12INVIVO.0.P.B_meme_format.meme
Transfac format	NDF2.H12INVIVO.0.P.B_transfac_format.txt
Homer format	NDF2.H12INVIVO.0.P.B_homer_format_0.001.txt NDF2.H12INVIVO.0.P.B_homer_format_0.0005.txt NDF2.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	461.0	91.0	394.0	54.0
02	320.0	184.0	487.0	9.0
03	0.0	1000.0	0.0	0.0
04	999.0	0.0	0.0	1.0
05	1.0	9.0	946.0	44.0
06	672.0	288.0	32.0	8.0
07	83.0	5.0	1.0	911.0
08	0.0	0.0	955.0	45.0
09	8.0	40.0	900.0	52.0
10	143.0	434.0	213.0	210.0
11	349.0	184.0	296.0	171.0

PFM

	A	C	G	T
01	0.461	0.091	0.394	0.054
02	0.32	0.184	0.487	0.009
03	0.0	1.0	0.0	0.0
04	0.999	0.0	0.0	0.001
05	0.001	0.009	0.946	0.044
06	0.672	0.288	0.032	0.008
07	0.083	0.005	0.001	0.911
08	0.0	0.0	0.955	0.045
09	0.008	0.04	0.9	0.052
10	0.143	0.434	0.213	0.21
11	0.349	0.184	0.296	0.171

PWM

	A	C	G	T
01	0.609	-0.999	0.452	-1.508
02	0.245	-0.304	0.663	-3.156
03	-4.982	1.381	-4.982	-4.982
04	1.38	-4.982	-4.982	-4.525
05	-4.525	-3.156	1.326	-1.706
06	0.984	0.141	-2.01	-3.253
07	-1.089	-3.622	-4.525	1.288
08	-4.982	-4.982	1.335	-1.684
09	-3.253	-1.797	1.276	-1.544
10	-0.553	0.549	-0.159	-0.173
11	0.332	-0.304	0.168	-0.377

Standard thresholds

P-value	Threshold
0.001	3.815285
0.0005	4.95839
0.0001	7.28196