TFAP4.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TFAP4.H12INVITRO.0.PSM.A
Gene (human)	TFAP4 (GeneCards)
Gene synonyms (human)	BHLHC41
Gene (mouse)
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	nhCAGCTGWTnn
GC content	48.63%
Information content (bits; total / per base)	14.947 / 1.246
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	7064

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 (33)	0.93	0.968	0.856	0.928	0.887	0.919	3.136	3.532	458.013	653.721

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.999	0.998	0.998	0.997	0.969	0.97
Overall, 8 experiments	best	1.0	1.0	1.0	1.0	0.995	0.994
Methyl HT-SELEX, 2 experiments	median	0.999	0.998	0.998	0.997	0.986	0.984
Methyl HT-SELEX, 2 experiments	best	0.999	0.999	0.999	0.998	0.989	0.988
Non-Methyl HT-SELEX, 6 experiments	median	0.998	0.997	0.997	0.995	0.955	0.956
Non-Methyl HT-SELEX, 6 experiments	best	1.0	1.0	1.0	1.0	0.995	0.994

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	100.0	3.834	0.396	0.344

TF superclass	Basic domains {1} (TFClass)
TF class	Basic helix-loop-helix factors (bHLH) {1.2} (TFClass)
TF family	bHLH-ZIP {1.2.6} (TFClass)
TF subfamily	AP4 {1.2.6.4} (TFClass)
TFClass ID	TFClass: 1.2.6.4.1
HGNC	HGNC:11745
MGI
EntrezGene (human)	GeneID:7023 (SSTAR profile)
EntrezGene (mouse)
UniProt ID (human)	TFAP4_HUMAN
UniProt ID (mouse)
UniProt AC (human)	Q01664 (TFClass)
UniProt AC (mouse)
GRECO-DB-TF	yes

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

PCM	TFAP4.H12INVITRO.0.PSM.A.pcm
PWM	TFAP4.H12INVITRO.0.PSM.A.pwm
PFM	TFAP4.H12INVITRO.0.PSM.A.pfm
Alignment	TFAP4.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	TFAP4.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	TFAP4.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	TFAP4.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	TFAP4.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	TFAP4.H12INVITRO.0.PSM.A_homer_format_0.001.txt TFAP4.H12INVITRO.0.PSM.A_homer_format_0.0005.txt TFAP4.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2361.25	1579.25	1868.25	1255.25
02	2085.0	1988.0	766.0	2225.0
03	0.0	7064.0	0.0	0.0
04	7064.0	0.0	0.0	0.0
05	0.0	0.0	7064.0	0.0
06	0.0	7064.0	0.0	0.0
07	0.0	0.0	0.0	7064.0
08	0.0	0.0	7064.0	0.0
09	2746.0	0.0	145.0	4173.0
10	28.25	24.25	57.25	6954.25
11	1771.25	2010.25	1073.25	2209.25
12	1721.25	1789.25	1666.25	1887.25

PFM

	A	C	G	T
01	0.334	0.224	0.264	0.178
02	0.295	0.281	0.108	0.315
03	0.0	1.0	0.0	0.0
04	1.0	0.0	0.0	0.0
05	0.0	0.0	1.0	0.0
06	0.0	1.0	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	1.0	0.0
09	0.389	0.0	0.021	0.591
10	0.004	0.003	0.008	0.984
11	0.251	0.285	0.152	0.313
12	0.244	0.253	0.236	0.267

PWM

	A	C	G	T
01	0.29	-0.112	0.056	-0.341
02	0.166	0.118	-0.834	0.231
03	-6.682	1.385	-6.682	-6.682
04	1.385	-6.682	-6.682	-6.682
05	-6.682	-6.682	1.385	-6.682
06	-6.682	1.385	-6.682	-6.682
07	-6.682	-6.682	-6.682	1.385
08	-6.682	-6.682	1.385	-6.682
09	0.441	-6.682	-2.486	0.859
10	-4.061	-4.202	-3.392	1.37
11	0.003	0.129	-0.497	0.224
12	-0.026	0.013	-0.058	0.066

Standard thresholds

P-value	Threshold
0.001	-1.63323
0.0005	2.027045
0.0001	4.808445