NDF1.H12INVIVO.1.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NDF1.H12INVIVO.1.S.C
Gene (human)	NEUROD1 (GeneCards)
Gene synonyms (human)	BHLHA3, NEUROD
Gene (mouse)	Neurod1
Gene synonyms (mouse)	Neurod
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	C

Motif length	12
Consensus	ndvCATATGKbv
GC content	48.22%
Information content (bits; total / per base)	11.257 / 0.938
Data sources	HT-SELEX
Aligned words	5244

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	6 (39)	0.761	0.851	0.669	0.755	0.733	0.836	2.112	2.633	98.921	247.538
Mouse	4 (21)	0.796	0.851	0.662	0.728	0.802	0.855	2.33	2.602	160.569	366.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 1 experiments	median	0.844	0.828	0.706	0.702	0.625	0.629
Non-Methyl HT-SELEX, 1 experiments	best	0.844	0.828	0.706	0.702	0.625	0.629

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: 1.2.3.4.1
HGNC	HGNC:7762
MGI	MGI:1339708
EntrezGene (human)	GeneID:4760 (SSTAR profile)
EntrezGene (mouse)	GeneID:18012 (SSTAR profile)
UniProt ID (human)	NDF1_HUMAN
UniProt ID (mouse)	NDF1_MOUSE
UniProt AC (human)	Q13562 (TFClass)
UniProt AC (mouse)	Q60867 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	6 human, 4 mouse
HT-SELEX	1
Methyl-HT-SELEX	0

PCM	NDF1.H12INVIVO.1.S.C.pcm
PWM	NDF1.H12INVIVO.1.S.C.pwm
PFM	NDF1.H12INVIVO.1.S.C.pfm
Alignment	NDF1.H12INVIVO.1.S.C.words.tsv
Threshold to P-value map	NDF1.H12INVIVO.1.S.C.thr
Motif in other formats
JASPAR format	NDF1.H12INVIVO.1.S.C_jaspar_format.txt
MEME format	NDF1.H12INVIVO.1.S.C_meme_format.meme
Transfac format	NDF1.H12INVIVO.1.S.C_transfac_format.txt
Homer format	NDF1.H12INVIVO.1.S.C_homer_format_0.001.txt NDF1.H12INVIVO.1.S.C_homer_format_0.0005.txt NDF1.H12INVIVO.1.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	849.25	1315.25	1655.25	1424.25
02	1587.25	476.25	2661.25	519.25
03	1941.0	922.0	1974.0	407.0
04	282.0	4251.0	654.0	57.0
05	4676.0	25.0	525.0	18.0
06	23.0	9.0	552.0	4660.0
07	4842.0	0.0	402.0	0.0
08	97.0	0.0	0.0	5147.0
09	0.0	3.0	5241.0	0.0
10	0.0	370.0	3638.0	1236.0
11	432.75	1408.75	992.75	2409.75
12	1178.5	1063.5	2203.5	798.5

PFM

	A	C	G	T
01	0.162	0.251	0.316	0.272
02	0.303	0.091	0.507	0.099
03	0.37	0.176	0.376	0.078
04	0.054	0.811	0.125	0.011
05	0.892	0.005	0.1	0.003
06	0.004	0.002	0.105	0.889
07	0.923	0.0	0.077	0.0
08	0.018	0.0	0.0	0.982
09	0.0	0.001	0.999	0.0
10	0.0	0.071	0.694	0.236
11	0.083	0.269	0.189	0.46
12	0.225	0.203	0.42	0.152

PWM

	A	C	G	T
01	-0.433	0.003	0.233	0.083
02	0.191	-1.01	0.707	-0.924
03	0.392	-0.351	0.409	-1.166
04	-1.531	1.175	-0.694	-3.1
05	1.27	-3.879	-0.913	-4.177
06	-3.956	-4.77	-0.863	1.267
07	1.305	-6.419	-1.178	-6.419
08	-2.584	-6.419	-6.419	1.366
09	-6.419	-5.543	1.384	-6.419
10	-6.419	-1.261	1.02	-0.059
11	-1.105	0.072	-0.278	0.608
12	-0.106	-0.209	0.519	-0.495

Standard thresholds

P-value	Threshold
0.001	4.352715
0.0005	5.470765
0.0001	7.50075