AP2A.H13CORE.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	AP2A.H13CORE.0.PSM.A
Gene (human)	TFAP2A (GeneCards)
Gene synonyms (human)	AP2TF, TFAP2
Gene (mouse)	Tfap2a
Gene synonyms (mouse)	Ap2tf, Tcfap2a
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	15
Consensus	nbGCCTSAGGSvRhn
GC content	65.65%
Information content (bits; total / per base)	13.914 / 0.928
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9912
Previous names	AP2A.H12CORE.0.PSM.A

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	10 (58)	0.892	0.96	0.788	0.912	0.785	0.861	2.327	2.911	201.054	426.319
Mouse	5 (34)	0.935	0.959	0.849	0.894	0.82	0.895	2.6	3.243	336.99	458.252

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 7 experiments	median	0.993	0.99	0.88	0.889	0.678	0.73
Overall, 7 experiments	best	0.999	0.998	0.998	0.996	0.996	0.994
Methyl HT-SELEX, 1 experiments	median	0.999	0.998	0.998	0.996	0.996	0.994
Methyl HT-SELEX, 1 experiments	best	0.999	0.998	0.998	0.996	0.996	0.994
Non-Methyl HT-SELEX, 6 experiments	median	0.986	0.979	0.857	0.865	0.676	0.718
Non-Methyl HT-SELEX, 6 experiments	best	0.997	0.994	0.994	0.991	0.991	0.985

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	10.08	5.166	0.426	0.221

TF superclass	Basic domains {1} (TFClass)
TF class	Basic helix-span-helix factors (bHSH) {1.3} (TFClass)
TF family	AP-2 {1.3.1} (TFClass)
TF subfamily	{1.3.1.0} (TFClass)
TFClass ID	TFClass: 1.3.1.0.1
HGNC	HGNC:11742
MGI	MGI:104671
EntrezGene (human)	GeneID:7020 (SSTAR profile)
EntrezGene (mouse)	GeneID:21418 (SSTAR profile)
UniProt ID (human)	AP2A_HUMAN
UniProt ID (mouse)	AP2A_MOUSE
UniProt AC (human)	P05549 (TFClass)
UniProt AC (mouse)	P34056 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	10 human, 5 mouse
HT-SELEX	6
Methyl-HT-SELEX	1
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	AP2A.H13CORE.0.PSM.A.pcm
PWM	AP2A.H13CORE.0.PSM.A.pwm
PFM	AP2A.H13CORE.0.PSM.A.pfm
Threshold to P-value map	AP2A.H13CORE.0.PSM.A.thr
Motif in other formats
JASPAR format	AP2A.H13CORE.0.PSM.A_jaspar_format.txt
MEME format	AP2A.H13CORE.0.PSM.A_meme_format.meme
Transfac format	AP2A.H13CORE.0.PSM.A_transfac_format.txt
Homer format	AP2A.H13CORE.0.PSM.A_homer_format_0.001.txt AP2A.H13CORE.0.PSM.A_homer_format_0.0005.txt AP2A.H13CORE.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2604.25	1427.25	2479.25	3401.25
02	1592.25	2474.25	1646.25	4199.25
03	152.0	983.0	8674.0	103.0
04	1.0	9906.0	4.0	1.0
05	1.0	9772.0	0.0	139.0
06	7.0	1304.0	302.0	8299.0
07	309.0	4116.0	5099.0	388.0
08	7370.0	213.0	2322.0	7.0
09	441.0	0.0	9471.0	0.0
10	1.0	0.0	9911.0	0.0
11	57.0	4561.0	5225.0	69.0
12	1459.0	4227.0	3034.0	1192.0
13	6133.0	447.0	1843.0	1489.0
14	2194.75	1935.75	1126.75	4654.75
15	2585.25	1704.25	3407.25	2215.25

PFM

	A	C	G	T
01	0.263	0.144	0.25	0.343
02	0.161	0.25	0.166	0.424
03	0.015	0.099	0.875	0.01
04	0.0	0.999	0.0	0.0
05	0.0	0.986	0.0	0.014
06	0.001	0.132	0.03	0.837
07	0.031	0.415	0.514	0.039
08	0.744	0.021	0.234	0.001
09	0.044	0.0	0.956	0.0
10	0.0	0.0	1.0	0.0
11	0.006	0.46	0.527	0.007
12	0.147	0.426	0.306	0.12
13	0.619	0.045	0.186	0.15
14	0.221	0.195	0.114	0.47
15	0.261	0.172	0.344	0.223

PWM

	A	C	G	T
01	0.05	-0.551	0.001	0.316
02	-0.442	-0.002	-0.408	0.527
03	-2.777	-0.923	1.252	-3.159
04	-6.622	1.385	-5.976	-6.622
05	-6.622	1.371	-6.983	-2.865
06	-5.586	-0.641	-2.098	1.208
07	-2.075	0.507	0.721	-1.849
08	1.089	-2.444	-0.065	-5.586
09	-1.722	-6.983	1.34	-6.983
10	-6.622	-6.983	1.385	-6.983
11	-3.734	0.61	0.746	-3.549
12	-0.529	0.534	0.202	-0.731
13	0.906	-1.708	-0.296	-0.509
14	-0.121	-0.247	-0.787	0.63
15	0.042	-0.374	0.318	-0.112

Standard thresholds

P-value	Threshold
0.001	2.44881
0.0005	3.97936
0.0001	6.91256