NFIA.H12RSNP.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NFIA.H12RSNP.0.P.B
Gene (human)	NFIA (GeneCards)
Gene synonyms (human)	KIAA1439
Gene (mouse)	Nfia
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	8
Consensus	bYTGGCWv
GC content	61.47%
Information content (bits; total / per base)	9.554 / 1.194
Data sources	ChIP-Seq
Aligned words	983

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	3 (21)	0.756	0.791	0.576	0.623	0.636	0.648	1.353	1.406	127.854	198.125
Mouse	6 (28)	0.779	0.888	0.662	0.81	0.647	0.773	1.475	1.919	46.997	85.721

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.977	0.962	0.96	0.941	0.829	0.837
Non-Methyl HT-SELEX, 2 experiments	best	0.987	0.978	0.981	0.968	0.889	0.891

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	100.0	4.137	0.28	0.14

TF superclass	beta-Hairpin exposed by an alpha/beta-scaffold {7} (TFClass)
TF class	SMAD/NF-1 DNA-binding domain factors {7.1} (TFClass)
TF family	NF-1 {7.1.2} (TFClass)
TF subfamily	{7.1.2.0} (TFClass)
TFClass ID	TFClass: 7.1.2.0.1
HGNC	HGNC:7784
MGI	MGI:108056
EntrezGene (human)	GeneID:4774 (SSTAR profile)
EntrezGene (mouse)	GeneID:18027 (SSTAR profile)
UniProt ID (human)	NFIA_HUMAN
UniProt ID (mouse)	NFIA_MOUSE
UniProt AC (human)	Q12857 (TFClass)
UniProt AC (mouse)	Q02780 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 6 mouse
HT-SELEX	2
Methyl-HT-SELEX	0

PCM	NFIA.H12RSNP.0.P.B.pcm
PWM	NFIA.H12RSNP.0.P.B.pwm
PFM	NFIA.H12RSNP.0.P.B.pfm
Alignment	NFIA.H12RSNP.0.P.B.words.tsv
Threshold to P-value map	NFIA.H12RSNP.0.P.B.thr
Motif in other formats
JASPAR format	NFIA.H12RSNP.0.P.B_jaspar_format.txt
MEME format	NFIA.H12RSNP.0.P.B_meme_format.meme
Transfac format	NFIA.H12RSNP.0.P.B_transfac_format.txt
Homer format	NFIA.H12RSNP.0.P.B_homer_format_0.001.txt NFIA.H12RSNP.0.P.B_homer_format_0.0005.txt NFIA.H12RSNP.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	73.0	521.0	170.0	219.0
02	37.0	412.0	8.0	526.0
03	1.0	2.0	2.0	978.0
04	2.0	0.0	977.0	4.0
05	5.0	4.0	969.0	5.0
06	24.0	950.0	5.0	4.0
07	605.0	49.0	28.0	301.0
08	179.0	244.0	493.0	67.0

PFM

	A	C	G	T
01	0.074	0.53	0.173	0.223
02	0.038	0.419	0.008	0.535
03	0.001	0.002	0.002	0.995
04	0.002	0.0	0.994	0.004
05	0.005	0.004	0.986	0.005
06	0.024	0.966	0.005	0.004
07	0.615	0.05	0.028	0.306
08	0.182	0.248	0.502	0.068

PWM

	A	C	G	T
01	-1.198	0.748	-0.365	-0.114
02	-1.855	0.514	-3.237	0.757
03	-4.51	-4.197	-4.197	1.376
04	-4.197	-4.967	1.375	-3.767
05	-3.606	-3.767	1.367	-3.606
06	-2.264	1.347	-3.606	-3.767
07	0.897	-1.585	-2.119	0.202
08	-0.314	-0.007	0.693	-1.281

Standard thresholds

P-value	Threshold
0.001	5.006745
0.0005	6.147985
0.0001	7.58777