NFIA.H12INVITRO.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NFIA.H12INVITRO.1.PS.A
Gene (human)	NFIA (GeneCards)
Gene synonyms (human)	KIAA1439
Gene (mouse)	Nfia
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	20
Consensus	nnTTGGCACGdTGCCAAvdn
GC content	53.52%
Information content (bits; total / per base)	26.384 / 1.319
Data sources	ChIP-Seq + HT-SELEX
Aligned words	361

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)	0.527	0.566	0.403	0.481	0.864	0.906	3.189	3.902	279.854	398.886
Mouse	6 (28)	0.503	0.509	0.343	0.358	0.635	0.68	1.572	1.83	17.422	38.824

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	1.0	1.0	0.988	0.989	0.835	0.864
Non-Methyl HT-SELEX, 2 experiments	best	1	1	1.0	1.0	0.898	0.916

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	100.0	4.471	0.277	0.181

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.H12INVITRO.1.PS.A.pcm
PWM	NFIA.H12INVITRO.1.PS.A.pwm
PFM	NFIA.H12INVITRO.1.PS.A.pfm
Alignment	NFIA.H12INVITRO.1.PS.A.words.tsv
Threshold to P-value map	NFIA.H12INVITRO.1.PS.A.thr
Motif in other formats
JASPAR format	NFIA.H12INVITRO.1.PS.A_jaspar_format.txt
MEME format	NFIA.H12INVITRO.1.PS.A_meme_format.meme
Transfac format	NFIA.H12INVITRO.1.PS.A_transfac_format.txt
Homer format	NFIA.H12INVITRO.1.PS.A_homer_format_0.001.txt NFIA.H12INVITRO.1.PS.A_homer_format_0.0005.txt NFIA.H12INVITRO.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	123.75	87.75	52.75	96.75
02	56.0	133.0	100.0	72.0
03	0.0	30.0	0.0	331.0
04	0.0	0.0	0.0	361.0
05	0.0	0.0	361.0	0.0
06	0.0	0.0	361.0	0.0
07	0.0	361.0	0.0	0.0
08	361.0	0.0	0.0	0.0
09	5.0	342.0	11.0	3.0
10	0.0	0.0	229.0	132.0
11	134.0	32.0	146.0	49.0
12	11.0	9.0	0.0	341.0
13	0.0	0.0	361.0	0.0
14	0.0	361.0	0.0	0.0
15	0.0	361.0	0.0	0.0
16	361.0	0.0	0.0	0.0
17	350.0	0.0	11.0	0.0
18	78.0	79.0	153.0	51.0
19	95.25	38.25	76.25	151.25
20	71.0	83.0	85.0	122.0

PFM

	A	C	G	T
01	0.343	0.243	0.146	0.268
02	0.155	0.368	0.277	0.199
03	0.0	0.083	0.0	0.917
04	0.0	0.0	0.0	1.0
05	0.0	0.0	1.0	0.0
06	0.0	0.0	1.0	0.0
07	0.0	1.0	0.0	0.0
08	1.0	0.0	0.0	0.0
09	0.014	0.947	0.03	0.008
10	0.0	0.0	0.634	0.366
11	0.371	0.089	0.404	0.136
12	0.03	0.025	0.0	0.945
13	0.0	0.0	1.0	0.0
14	0.0	1.0	0.0	0.0
15	0.0	1.0	0.0	0.0
16	1.0	0.0	0.0	0.0
17	0.97	0.0	0.03	0.0
18	0.216	0.219	0.424	0.141
19	0.264	0.106	0.211	0.419
20	0.197	0.23	0.235	0.338

PWM

	A	C	G	T
01	0.311	-0.028	-0.526	0.068
02	-0.467	0.383	0.101	-0.222
03	-4.132	-1.07	-4.132	1.288
04	-4.132	-4.132	-4.132	1.374
05	-4.132	-4.132	1.374	-4.132
06	-4.132	-4.132	1.374	-4.132
07	-4.132	1.374	-4.132	-4.132
08	1.374	-4.132	-4.132	-4.132
09	-2.651	1.32	-1.995	-3.021
10	-4.132	-4.132	0.921	0.375
11	0.39	-1.008	0.475	-0.597
12	-1.995	-2.17	-4.132	1.317
13	-4.132	-4.132	1.374	-4.132
14	-4.132	1.374	-4.132	-4.132
15	-4.132	1.374	-4.132	-4.132
16	1.374	-4.132	-4.132	-4.132
17	1.343	-4.132	-1.995	-4.132
18	-0.143	-0.131	0.521	-0.558
19	0.053	-0.837	-0.166	0.51
20	-0.236	-0.082	-0.059	0.297

Standard thresholds

P-value	Threshold
0.001	-5.82204
0.0005	-3.79864
0.0001	0.18151