AP2A.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	AP2A.H12INVITRO.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	16
Consensus	nGCCTSAGGCvWWdnn
GC content	63.64%
Information content (bits; total / per base)	14.95 / 0.934
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	8184

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)	0.887	0.957	0.78	0.905	0.759	0.845	2.234	2.762	181.549	395.796
Mouse	5 (34)	0.933	0.956	0.846	0.892	0.795	0.883	2.445	3.146	328.561	435.137

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 7 experiments	median	0.994	0.991	0.953	0.946	0.76	0.792
Overall, 7 experiments	best	0.999	0.999	0.997	0.996	0.995	0.992
Methyl HT-SELEX, 1 experiments	median	0.998	0.997	0.997	0.995	0.995	0.992
Methyl HT-SELEX, 1 experiments	best	0.998	0.997	0.997	0.995	0.995	0.992
Non-Methyl HT-SELEX, 6 experiments	median	0.992	0.988	0.916	0.918	0.719	0.761
Non-Methyl HT-SELEX, 6 experiments	best	0.999	0.999	0.997	0.996	0.989	0.984

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	7.35	4.342	0.406	0.22

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

PCM	AP2A.H12INVITRO.0.PSM.A.pcm
PWM	AP2A.H12INVITRO.0.PSM.A.pwm
PFM	AP2A.H12INVITRO.0.PSM.A.pfm
Alignment	AP2A.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	AP2A.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	AP2A.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	AP2A.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	AP2A.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	AP2A.H12INVITRO.0.PSM.A_homer_format_0.001.txt AP2A.H12INVITRO.0.PSM.A_homer_format_0.0005.txt AP2A.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1609.75	2770.75	1867.75	1935.75
02	48.75	2254.75	5835.75	44.75
03	2.0	8182.0	0.0	0.0
04	0.0	8161.0	1.0	22.0
05	0.0	1498.0	152.0	6534.0
06	45.0	3775.0	4280.0	84.0
07	6608.0	96.0	1479.0	1.0
08	8.0	0.0	8176.0	0.0
09	0.0	0.0	8184.0	0.0
10	12.0	5223.0	2943.0	6.0
11	1436.0	2601.0	2850.0	1297.0
12	5975.0	318.0	650.0	1241.0
13	1460.0	1068.0	446.0	5210.0
14	2530.0	918.0	2122.0	2614.0
15	1642.25	1772.25	1496.25	3273.25
16	1910.75	1875.75	2331.75	2065.75

PFM

	A	C	G	T
01	0.197	0.339	0.228	0.237
02	0.006	0.276	0.713	0.005
03	0.0	1.0	0.0	0.0
04	0.0	0.997	0.0	0.003
05	0.0	0.183	0.019	0.798
06	0.005	0.461	0.523	0.01
07	0.807	0.012	0.181	0.0
08	0.001	0.0	0.999	0.0
09	0.0	0.0	1.0	0.0
10	0.001	0.638	0.36	0.001
11	0.175	0.318	0.348	0.158
12	0.73	0.039	0.079	0.152
13	0.178	0.13	0.054	0.637
14	0.309	0.112	0.259	0.319
15	0.201	0.217	0.183	0.4
16	0.233	0.229	0.285	0.252

PWM

	A	C	G	T
01	-0.24	0.303	-0.091	-0.055
02	-3.693	0.097	1.047	-3.775
03	-6.177	1.385	-6.813	-6.813
04	-6.813	1.383	-6.445	-4.436
05	-6.813	-0.311	-2.586	1.16
06	-3.769	0.612	0.737	-3.167
07	1.172	-3.037	-0.324	-6.445
08	-5.297	-6.813	1.384	-6.813
09	-6.813	-6.813	1.385	-6.813
10	-4.968	0.937	0.363	-5.514
11	-0.354	0.24	0.331	-0.455
12	1.071	-1.856	-1.144	-0.499
13	-0.337	-0.649	-1.519	0.934
14	0.212	-0.8	0.036	0.245
15	-0.22	-0.143	-0.313	0.469
16	-0.068	-0.087	0.131	0.01

Standard thresholds

P-value	Threshold
0.001	0.88711
0.0005	2.56731
0.0001	6.32796