PAX3.H12INVITRO.3.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX3.H12INVITRO.3.S.B
Gene (human)	PAX3 (GeneCards)
Gene synonyms (human)	HUP2
Gene (mouse)	Pax3
Gene synonyms (mouse)	Pax-3
LOGO
LOGO (reverse complement)
Motif subtype	3
Quality	B

Motif length	20
Consensus	nnTAATCGATTAvbnnnnnn
GC content	30.45%
Information content (bits; total / per base)	18.473 / 0.924
Data sources	HT-SELEX
Aligned words	2491

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)	0.544	0.697	0.4	0.65	0.43	0.665	1.095	3.195	25.569	210.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.987	0.982	0.911	0.9	0.781	0.794
Overall, 4 experiments	best	0.999	0.999	0.983	0.982	0.811	0.815
Methyl HT-SELEX, 1 experiments	median	0.986	0.981	0.902	0.891	0.792	0.785
Methyl HT-SELEX, 1 experiments	best	0.986	0.981	0.902	0.891	0.792	0.785
Non-Methyl HT-SELEX, 3 experiments	median	0.988	0.983	0.92	0.909	0.77	0.803
Non-Methyl HT-SELEX, 3 experiments	best	0.999	0.999	0.983	0.982	0.811	0.815

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.H12INVITRO.3.S.B.pcm
PWM	PAX3.H12INVITRO.3.S.B.pwm
PFM	PAX3.H12INVITRO.3.S.B.pfm
Alignment	PAX3.H12INVITRO.3.S.B.words.tsv
Threshold to P-value map	PAX3.H12INVITRO.3.S.B.thr
Motif in other formats
JASPAR format	PAX3.H12INVITRO.3.S.B_jaspar_format.txt
MEME format	PAX3.H12INVITRO.3.S.B_meme_format.meme
Transfac format	PAX3.H12INVITRO.3.S.B_transfac_format.txt
Homer format	PAX3.H12INVITRO.3.S.B_homer_format_0.001.txt PAX3.H12INVITRO.3.S.B_homer_format_0.0005.txt PAX3.H12INVITRO.3.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	646.0	377.0	895.0	573.0
02	380.25	598.25	594.25	918.25
03	70.0	35.0	15.0	2371.0
04	2484.0	3.0	4.0	0.0
05	2486.0	0.0	1.0	4.0
06	0.0	0.0	1.0	2490.0
07	0.0	1939.0	0.0	552.0
08	535.0	0.0	1956.0	0.0
09	2490.0	1.0	0.0	0.0
10	1.0	0.0	1.0	2489.0
11	6.0	6.0	3.0	2476.0
12	2394.0	13.0	55.0	29.0
13	1051.0	536.0	713.0	191.0
14	296.0	768.0	376.0	1051.0
15	565.0	561.0	466.0	899.0
16	954.0	454.0	532.0	551.0
17	733.0	532.0	487.0	739.0
18	666.0	680.0	416.0	729.0
19	841.5	645.5	398.5	605.5
20	800.0	692.0	414.0	585.0

PFM

	A	C	G	T
01	0.259	0.151	0.359	0.23
02	0.153	0.24	0.239	0.369
03	0.028	0.014	0.006	0.952
04	0.997	0.001	0.002	0.0
05	0.998	0.0	0.0	0.002
06	0.0	0.0	0.0	1.0
07	0.0	0.778	0.0	0.222
08	0.215	0.0	0.785	0.0
09	1.0	0.0	0.0	0.0
10	0.0	0.0	0.0	0.999
11	0.002	0.002	0.001	0.994
12	0.961	0.005	0.022	0.012
13	0.422	0.215	0.286	0.077
14	0.119	0.308	0.151	0.422
15	0.227	0.225	0.187	0.361
16	0.383	0.182	0.214	0.221
17	0.294	0.214	0.196	0.297
18	0.267	0.273	0.167	0.293
19	0.338	0.259	0.16	0.243
20	0.321	0.278	0.166	0.235

PWM

	A	C	G	T
01	0.037	-0.5	0.362	-0.083
02	-0.491	-0.04	-0.047	0.387
03	-2.161	-2.828	-3.607	1.335
04	1.381	-4.837	-4.653	-5.767
05	1.382	-5.767	-5.354	-4.653
06	-5.767	-5.767	-5.354	1.384
07	-5.767	1.134	-5.767	-0.12
08	-0.151	-5.767	1.142	-5.767
09	1.384	-5.354	-5.767	-5.767
10	-5.354	-5.767	-5.354	1.383
11	-4.363	-4.363	-4.837	1.378
12	1.344	-3.732	-2.395	-3.005
13	0.522	-0.15	0.135	-1.175
14	-0.74	0.209	-0.503	0.522
15	-0.097	-0.104	-0.289	0.366
16	0.425	-0.315	-0.157	-0.122
17	0.163	-0.157	-0.245	0.171
18	0.067	0.088	-0.402	0.157
19	0.3	0.036	-0.445	-0.028
20	0.25	0.105	-0.407	-0.062

Standard thresholds

P-value	Threshold
0.001	-1.83774
0.0005	0.03186
0.0001	3.81831