PAX3.H12INVITRO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX3.H12INVITRO.1.SM.B
Gene (human)	PAX3 (GeneCards)
Gene synonyms (human)	HUP2
Gene (mouse)	Pax3
Gene synonyms (mouse)	Pax-3
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	19
Consensus	hdbYRATTAGTCACGSYhn
GC content	42.52%
Information content (bits; total / per base)	21.669 / 1.14
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	671

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)	0.812	0.828	0.736	0.762	0.745	0.778	2.721	3.011	158.398	197.62

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.872	0.834	0.852	0.819	0.803	0.78
Overall, 4 experiments	best	1.0	1.0	0.995	0.994	0.962	0.956
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	0.995	0.994	0.947	0.943
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.995	0.994	0.947	0.943
Non-Methyl HT-SELEX, 3 experiments	median	0.745	0.67	0.711	0.647	0.659	0.616
Non-Methyl HT-SELEX, 3 experiments	best	0.999	0.999	0.993	0.99	0.962	0.956

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.1.SM.B.pcm
PWM	PAX3.H12INVITRO.1.SM.B.pwm
PFM	PAX3.H12INVITRO.1.SM.B.pfm
Alignment	PAX3.H12INVITRO.1.SM.B.words.tsv
Threshold to P-value map	PAX3.H12INVITRO.1.SM.B.thr
Motif in other formats
JASPAR format	PAX3.H12INVITRO.1.SM.B_jaspar_format.txt
MEME format	PAX3.H12INVITRO.1.SM.B_meme_format.meme
Transfac format	PAX3.H12INVITRO.1.SM.B_transfac_format.txt
Homer format	PAX3.H12INVITRO.1.SM.B_homer_format_0.001.txt PAX3.H12INVITRO.1.SM.B_homer_format_0.0005.txt PAX3.H12INVITRO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	302.75	121.75	114.75	131.75
02	281.75	120.75	146.75	121.75
03	72.0	185.0	111.0	303.0
04	40.0	247.0	51.0	333.0
05	454.0	32.0	178.0	7.0
06	635.0	10.0	12.0	14.0
07	1.0	10.0	4.0	656.0
08	2.0	17.0	2.0	650.0
09	592.0	14.0	59.0	6.0
10	1.0	0.0	669.0	1.0
11	1.0	1.0	0.0	669.0
12	0.0	662.0	0.0	9.0
13	658.0	1.0	12.0	0.0
14	1.0	662.0	1.0	7.0
15	2.0	1.0	667.0	1.0
16	6.0	362.0	301.0	2.0
17	71.0	74.0	24.0	502.0
18	146.0	153.0	83.0	289.0
19	208.5	149.5	162.5	150.5

PFM

	A	C	G	T
01	0.451	0.181	0.171	0.196
02	0.42	0.18	0.219	0.181
03	0.107	0.276	0.165	0.452
04	0.06	0.368	0.076	0.496
05	0.677	0.048	0.265	0.01
06	0.946	0.015	0.018	0.021
07	0.001	0.015	0.006	0.978
08	0.003	0.025	0.003	0.969
09	0.882	0.021	0.088	0.009
10	0.001	0.0	0.997	0.001
11	0.001	0.001	0.0	0.997
12	0.0	0.987	0.0	0.013
13	0.981	0.001	0.018	0.0
14	0.001	0.987	0.001	0.01
15	0.003	0.001	0.994	0.001
16	0.009	0.539	0.449	0.003
17	0.106	0.11	0.036	0.748
18	0.218	0.228	0.124	0.431
19	0.311	0.223	0.242	0.224

PWM

	A	C	G	T
01	0.586	-0.317	-0.375	-0.239
02	0.515	-0.325	-0.132	-0.317
03	-0.833	0.097	-0.408	0.587
04	-1.403	0.384	-1.169	0.681
05	0.99	-1.617	0.059	-2.977
06	1.324	-2.679	-2.52	-2.383
07	-4.166	-2.679	-3.405	1.357
08	-3.844	-2.208	-3.844	1.347
09	1.254	-2.383	-1.027	-3.1
10	-4.166	-4.645	1.376	-4.166
11	-4.166	-4.166	-4.645	1.376
12	-4.645	1.366	-4.645	-2.769
13	1.36	-4.166	-2.52	-4.645
14	-4.166	1.366	-4.166	-2.977
15	-3.844	-4.166	1.373	-4.166
16	-3.1	0.764	0.58	-3.844
17	-0.847	-0.806	-1.888	1.09
18	-0.137	-0.091	-0.694	0.54
19	0.216	-0.114	-0.031	-0.107

Standard thresholds

P-value	Threshold
0.001	-1.70839
0.0005	-0.07054
0.0001	3.40906