NDF2.H12INVITRO.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NDF2.H12INVITRO.1.S.B
Gene (human)	NEUROD2 (GeneCards)
Gene synonyms (human)	BHLHA1, NDRF
Gene (mouse)	Neurod2
Gene synonyms (mouse)	Ndrf
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	11
Consensus	vvCATATGKKn
GC content	43.5%
Information content (bits; total / per base)	12.613 / 1.147
Data sources	HT-SELEX
Aligned words	985

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)	0.777	0.836	0.633	0.68	0.773	0.83	2.228	2.528	96.091	138.26

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.689	0.666	0.613	0.6	0.572	0.567
Non-Methyl HT-SELEX, 2 experiments	best	0.691	0.67	0.613	0.602	0.572	0.567

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.H12INVITRO.1.S.B.pcm
PWM	NDF2.H12INVITRO.1.S.B.pwm
PFM	NDF2.H12INVITRO.1.S.B.pfm
Alignment	NDF2.H12INVITRO.1.S.B.words.tsv
Threshold to P-value map	NDF2.H12INVITRO.1.S.B.thr
Motif in other formats
JASPAR format	NDF2.H12INVITRO.1.S.B_jaspar_format.txt
MEME format	NDF2.H12INVITRO.1.S.B_meme_format.meme
Transfac format	NDF2.H12INVITRO.1.S.B_transfac_format.txt
Homer format	NDF2.H12INVITRO.1.S.B_homer_format_0.001.txt NDF2.H12INVITRO.1.S.B_homer_format_0.0005.txt NDF2.H12INVITRO.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	307.75	167.75	367.75	141.75
02	293.5	196.5	438.5	56.5
03	31.0	941.0	9.0	4.0
04	958.0	0.0	27.0	0.0
05	2.0	0.0	34.0	949.0
06	949.0	0.0	36.0	0.0
07	6.0	0.0	0.0	979.0
08	0.0	0.0	985.0	0.0
09	0.0	65.0	605.0	315.0
10	111.5	128.5	143.5	601.5
11	270.0	243.0	326.0	146.0

PFM

	A	C	G	T
01	0.312	0.17	0.373	0.144
02	0.298	0.199	0.445	0.057
03	0.031	0.955	0.009	0.004
04	0.973	0.0	0.027	0.0
05	0.002	0.0	0.035	0.963
06	0.963	0.0	0.037	0.0
07	0.006	0.0	0.0	0.994
08	0.0	0.0	1.0	0.0
09	0.0	0.066	0.614	0.32
10	0.113	0.13	0.146	0.611
11	0.274	0.247	0.331	0.148

PWM

	A	C	G	T
01	0.222	-0.381	0.399	-0.547
02	0.174	-0.224	0.574	-1.449
03	-2.025	1.335	-3.141	-3.769
04	1.353	-4.969	-2.156	-4.969
05	-4.199	-4.969	-1.938	1.344
06	1.344	-4.969	-1.883	-4.969
07	-3.469	-4.969	-4.969	1.375
08	-4.969	-4.969	1.381	-4.969
09	-4.969	-1.313	0.895	0.245
10	-0.784	-0.644	-0.535	0.889
11	0.091	-0.013	0.279	-0.518

Standard thresholds

P-value	Threshold
0.001	3.476535
0.0005	4.686975
0.0001	7.440735