PAX3.H12INVIVO.2.P.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX3.H12INVIVO.2.P.C
Gene (human)	PAX3 (GeneCards)
Gene synonyms (human)	HUP2
Gene (mouse)	Pax3
Gene synonyms (mouse)	Pax-3
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	C

Motif length	12
Consensus	ndvWMATKSRWW
GC content	33.43%
Information content (bits; total / per base)	8.253 / 0.688
Data sources	ChIP-Seq
Aligned words	857

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
Mouse	6 (39)	0.608	0.756	0.469	0.691	0.578	0.772	1.509	3.065	35.119	185.456

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.965	0.952	0.897	0.875	0.794	0.785
Overall, 4 experiments	best	0.997	0.995	0.972	0.967	0.806	0.817
Methyl HT-SELEX, 1 experiments	median	0.971	0.961	0.898	0.879	0.801	0.785
Methyl HT-SELEX, 1 experiments	best	0.971	0.961	0.898	0.879	0.801	0.785
Non-Methyl HT-SELEX, 3 experiments	median	0.959	0.942	0.895	0.87	0.786	0.784
Non-Methyl HT-SELEX, 3 experiments	best	0.997	0.995	0.972	0.967	0.806	0.817

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Paired box factors {3.2} (TFClass)
TF family	PD+HD {3.2.1} (TFClass)
TF subfamily	PAX3-like {3.2.1.1} (TFClass)
TFClass ID	TFClass: 3.2.1.1.1
HGNC	HGNC:8617
MGI	MGI:97487
EntrezGene (human)	GeneID:5077 (SSTAR profile)
EntrezGene (mouse)	GeneID:18505 (SSTAR profile)
UniProt ID (human)	PAX3_HUMAN
UniProt ID (mouse)	PAX3_MOUSE
UniProt AC (human)	P23760 (TFClass)
UniProt AC (mouse)	P24610 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 6 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	PAX3.H12INVIVO.2.P.C.pcm
PWM	PAX3.H12INVIVO.2.P.C.pwm
PFM	PAX3.H12INVIVO.2.P.C.pfm
Alignment	PAX3.H12INVIVO.2.P.C.words.tsv
Threshold to P-value map	PAX3.H12INVIVO.2.P.C.thr
Motif in other formats
JASPAR format	PAX3.H12INVIVO.2.P.C_jaspar_format.txt
MEME format	PAX3.H12INVIVO.2.P.C_meme_format.meme
Transfac format	PAX3.H12INVIVO.2.P.C_transfac_format.txt
Homer format	PAX3.H12INVIVO.2.P.C_homer_format_0.001.txt PAX3.H12INVIVO.2.P.C_homer_format_0.0005.txt PAX3.H12INVIVO.2.P.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	233.0	123.0	301.0	200.0
02	177.0	101.0	344.0	235.0
03	154.0	283.0	294.0	126.0
04	258.0	21.0	22.0	556.0
05	606.0	197.0	40.0	14.0
06	819.0	28.0	6.0	4.0
07	13.0	43.0	60.0	741.0
08	18.0	45.0	225.0	569.0
09	41.0	102.0	660.0	54.0
10	569.0	90.0	123.0	75.0
11	128.0	82.0	98.0	549.0
12	98.0	76.0	74.0	609.0

PFM

	A	C	G	T
01	0.272	0.144	0.351	0.233
02	0.207	0.118	0.401	0.274
03	0.18	0.33	0.343	0.147
04	0.301	0.025	0.026	0.649
05	0.707	0.23	0.047	0.016
06	0.956	0.033	0.007	0.005
07	0.015	0.05	0.07	0.865
08	0.021	0.053	0.263	0.664
09	0.048	0.119	0.77	0.063
10	0.664	0.105	0.144	0.088
11	0.149	0.096	0.114	0.641
12	0.114	0.089	0.086	0.711

PWM

	A	C	G	T
01	0.083	-0.549	0.338	-0.068
02	-0.189	-0.743	0.471	0.092
03	-0.327	0.276	0.314	-0.525
04	0.184	-2.253	-2.21	0.949
05	1.035	-0.083	-1.645	-2.622
06	1.335	-1.984	-3.335	-3.637
07	-2.688	-1.575	-1.253	1.235
08	-2.395	-1.531	0.049	0.972
09	-1.621	-0.734	1.12	-1.355
10	0.972	-0.857	-0.549	-1.035
11	-0.51	-0.948	-0.773	0.936
12	-0.773	-1.022	-1.048	1.04

Standard thresholds

P-value	Threshold
0.001	4.96361
0.0005	5.65711
0.0001	7.087645