NGN2.H12INVIVO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NGN2.H12INVIVO.1.SM.B
Gene (human)	NEUROG2 (GeneCards)
Gene synonyms (human)	ATOH4, BHLHA8, NGN2
Gene (mouse)	Neurog2
Gene synonyms (mouse)	Ath4a, Atoh4, Ngn2
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	11
Consensus	vvCATATGTYn
GC content	38.53%
Information content (bits; total / per base)	13.131 / 1.194
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	6915

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
Human	12 (84)	0.843	0.878	0.672	0.73	0.8	0.857	2.274	2.682	72.685	134.721
Mouse	5 (31)	0.858	0.887	0.669	0.72	0.842	0.873	2.453	2.687	133.678	217.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.953	0.947	0.776	0.786	0.648	0.674
Overall, 5 experiments	best	0.986	0.981	0.86	0.859	0.708	0.73
Methyl HT-SELEX, 1 experiments	median	0.834	0.834	0.671	0.687	0.584	0.609
Methyl HT-SELEX, 1 experiments	best	0.834	0.834	0.671	0.687	0.584	0.609
Non-Methyl HT-SELEX, 4 experiments	median	0.958	0.952	0.782	0.792	0.651	0.678
Non-Methyl HT-SELEX, 4 experiments	best	0.986	0.981	0.86	0.859	0.708	0.73

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: 1.2.3.4.6
HGNC	HGNC:13805
MGI	MGI:109619
EntrezGene (human)	GeneID:63973 (SSTAR profile)
EntrezGene (mouse)	GeneID:11924 (SSTAR profile)
UniProt ID (human)	NGN2_HUMAN
UniProt ID (mouse)	NGN2_MOUSE
UniProt AC (human)	Q9H2A3 (TFClass)
UniProt AC (mouse)	P70447 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	12 human, 5 mouse
HT-SELEX	4
Methyl-HT-SELEX	1

PCM	NGN2.H12INVIVO.1.SM.B.pcm
PWM	NGN2.H12INVIVO.1.SM.B.pwm
PFM	NGN2.H12INVIVO.1.SM.B.pfm
Alignment	NGN2.H12INVIVO.1.SM.B.words.tsv
Threshold to P-value map	NGN2.H12INVIVO.1.SM.B.thr
Motif in other formats
JASPAR format	NGN2.H12INVIVO.1.SM.B_jaspar_format.txt
MEME format	NGN2.H12INVIVO.1.SM.B_meme_format.meme
Transfac format	NGN2.H12INVIVO.1.SM.B_transfac_format.txt
Homer format	NGN2.H12INVIVO.1.SM.B_homer_format_0.001.txt NGN2.H12INVIVO.1.SM.B_homer_format_0.0005.txt NGN2.H12INVIVO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2588.5	925.5	2605.5	795.5
02	2245.75	1839.75	2476.75	352.75
03	242.0	6443.0	123.0	107.0
04	6733.0	5.0	100.0	77.0
05	0.0	1.0	258.0	6656.0
06	6753.0	162.0	0.0	0.0
07	0.0	0.0	0.0	6915.0
08	0.0	0.0	6915.0	0.0
09	62.0	373.0	765.0	5715.0
10	177.75	2513.75	374.75	3848.75
11	2050.75	1871.75	1551.75	1440.75

PFM

	A	C	G	T
01	0.374	0.134	0.377	0.115
02	0.325	0.266	0.358	0.051
03	0.035	0.932	0.018	0.015
04	0.974	0.001	0.014	0.011
05	0.0	0.0	0.037	0.963
06	0.977	0.023	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	1.0	0.0
09	0.009	0.054	0.111	0.826
10	0.026	0.364	0.054	0.557
11	0.297	0.271	0.224	0.208

PWM

	A	C	G	T
01	0.403	-0.624	0.41	-0.775
02	0.261	0.062	0.359	-1.584
03	-1.958	1.315	-2.626	-2.763
04	1.359	-5.481	-2.829	-3.084
05	-6.663	-6.29	-1.895	1.347
06	1.362	-2.355	-6.663	-6.663
07	-6.663	-6.663	-6.663	1.385
08	-6.663	-6.663	1.385	-6.663
09	-3.294	-1.529	-0.814	1.195
10	-2.264	0.374	-1.524	0.8
11	0.171	0.079	-0.108	-0.182

Standard thresholds

P-value	Threshold
0.001	2.93951
0.0005	4.34036
0.0001	7.105225