NDF1.H12INVITRO.1.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NDF1.H12INVITRO.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	nvvCATATGKbn
GC content	45.51%
Information content (bits; total / per base)	13.12 / 1.093
Data sources	HT-SELEX
Aligned words	1509

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)	0.749	0.841	0.634	0.713	0.684	0.804	1.815	2.336	90.721	247.347
Mouse	4 (21)	0.779	0.828	0.612	0.658	0.756	0.813	1.997	2.217	152.678	328.658

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 1 experiments	median	0.853	0.838	0.706	0.706	0.617	0.628
Non-Methyl HT-SELEX, 1 experiments	best	0.853	0.838	0.706	0.706	0.617	0.628

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.H12INVITRO.1.S.C.pcm
PWM	NDF1.H12INVITRO.1.S.C.pwm
PFM	NDF1.H12INVITRO.1.S.C.pfm
Alignment	NDF1.H12INVITRO.1.S.C.words.tsv
Threshold to P-value map	NDF1.H12INVITRO.1.S.C.thr
Motif in other formats
JASPAR format	NDF1.H12INVITRO.1.S.C_jaspar_format.txt
MEME format	NDF1.H12INVITRO.1.S.C_meme_format.meme
Transfac format	NDF1.H12INVITRO.1.S.C_transfac_format.txt
Homer format	NDF1.H12INVITRO.1.S.C_homer_format_0.001.txt NDF1.H12INVITRO.1.S.C_homer_format_0.0005.txt NDF1.H12INVITRO.1.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	252.75	354.75	464.75	436.75
02	555.0	176.0	656.0	122.0
03	609.0	241.0	587.0	72.0
04	12.0	1454.0	40.0	3.0
05	1494.0	1.0	13.0	1.0
06	0.0	0.0	24.0	1485.0
07	1485.0	0.0	24.0	0.0
08	11.0	0.0	0.0	1498.0
09	0.0	0.0	1509.0	0.0
10	0.0	100.0	1005.0	404.0
11	138.5	396.5	272.5	701.5
12	325.5	334.5	587.5	261.5

PFM

	A	C	G	T
01	0.167	0.235	0.308	0.289
02	0.368	0.117	0.435	0.081
03	0.404	0.16	0.389	0.048
04	0.008	0.964	0.027	0.002
05	0.99	0.001	0.009	0.001
06	0.0	0.0	0.016	0.984
07	0.984	0.0	0.016	0.0
08	0.007	0.0	0.0	0.993
09	0.0	0.0	1.0	0.0
10	0.0	0.066	0.666	0.268
11	0.092	0.263	0.181	0.465
12	0.216	0.222	0.389	0.173

PWM

	A	C	G	T
01	-0.398	-0.061	0.208	0.146
02	0.385	-0.757	0.551	-1.119
03	0.477	-0.445	0.44	-1.636
04	-3.311	1.346	-2.204	-4.363
05	1.373	-4.898	-3.241	-4.898
06	-5.334	-5.334	-2.686	1.367
07	1.367	-5.334	-2.686	-5.334
08	-3.386	-5.334	-5.334	1.375
09	-5.334	-5.334	1.383	-5.334
10	-5.334	-1.314	0.977	0.068
11	-0.994	0.05	-0.323	0.618
12	-0.147	-0.12	0.441	-0.364

Standard thresholds

P-value	Threshold
0.001	2.994395
0.0005	4.184955
0.0001	7.25763