TFAP4.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TFAP4.H12RSNP.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	11
Consensus	CAGCTGdKbbb
GC content	57.9%
Information content (bits; total / per base)	12.971 / 1.179
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	999

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)	0.936	0.967	0.845	0.922	0.906	0.932	3.065	3.654	493.699	730.824

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.997	0.994	0.995	0.992	0.973	0.971
Overall, 8 experiments	best	0.999	0.998	0.999	0.998	0.994	0.993
Methyl HT-SELEX, 2 experiments	median	0.997	0.994	0.995	0.992	0.987	0.982
Methyl HT-SELEX, 2 experiments	best	0.997	0.995	0.996	0.993	0.99	0.986
Non-Methyl HT-SELEX, 6 experiments	median	0.997	0.994	0.993	0.988	0.96	0.958
Non-Methyl HT-SELEX, 6 experiments	best	0.999	0.998	0.999	0.998	0.994	0.993

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	100.0	4.066	0.41	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.H12RSNP.0.PSM.A.pcm
PWM	TFAP4.H12RSNP.0.PSM.A.pwm
PFM	TFAP4.H12RSNP.0.PSM.A.pfm
Alignment	TFAP4.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	TFAP4.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	TFAP4.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	TFAP4.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	TFAP4.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	TFAP4.H12RSNP.0.PSM.A_homer_format_0.001.txt TFAP4.H12RSNP.0.PSM.A_homer_format_0.0005.txt TFAP4.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	0.0	996.0	3.0	0.0
02	995.0	1.0	0.0	3.0
03	0.0	3.0	980.0	16.0
04	16.0	977.0	4.0	2.0
05	2.0	0.0	1.0	996.0
06	0.0	1.0	996.0	2.0
07	198.0	117.0	243.0	441.0
08	14.0	124.0	217.0	644.0
09	70.0	228.0	211.0	490.0
10	118.0	405.0	184.0	292.0
11	95.0	472.0	200.0	232.0

PFM

	A	C	G	T
01	0.0	0.997	0.003	0.0
02	0.996	0.001	0.0	0.003
03	0.0	0.003	0.981	0.016
04	0.016	0.978	0.004	0.002
05	0.002	0.0	0.001	0.997
06	0.0	0.001	0.997	0.002
07	0.198	0.117	0.243	0.441
08	0.014	0.124	0.217	0.645
09	0.07	0.228	0.211	0.49
10	0.118	0.405	0.184	0.292
11	0.095	0.472	0.2	0.232

PWM

	A	C	G	T
01	-4.981	1.378	-3.974	-4.981
02	1.377	-4.524	-4.981	-3.974
03	-4.981	-3.974	1.362	-2.652
04	-2.652	1.359	-3.782	-4.212
05	-4.212	-4.981	-4.524	1.378
06	-4.981	-4.524	1.378	-4.212
07	-0.23	-0.751	-0.027	0.566
08	-2.772	-0.693	-0.14	0.943
09	-1.254	-0.09	-0.167	0.671
10	-0.742	0.481	-0.303	0.155
11	-0.955	0.633	-0.22	-0.073

Standard thresholds

P-value	Threshold
0.001	3.143095
0.0005	4.12981
0.0001	7.530925