PAX7.H12INVIVO.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX7.H12INVIVO.1.S.B
Gene (human)	PAX7 (GeneCards)
Gene synonyms (human)	HUP1
Gene (mouse)	Pax7
Gene synonyms (mouse)	Pax-7
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	14
Consensus	nhAATCGATTAvbn
GC content	31.43%
Information content (bits; total / per base)	14.675 / 1.048
Data sources	HT-SELEX
Aligned words	8390

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	3 (21)	0.704	0.98	0.55	0.972	0.581	0.973	1.483	6.544	53.602	969.292

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.998	0.997	0.986	0.982	0.871	0.88
Overall, 8 experiments	best	1.0	0.999	0.999	0.999	0.996	0.995
Methyl HT-SELEX, 2 experiments	median	0.998	0.997	0.988	0.985	0.946	0.94
Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.998	0.996	0.985	0.982
Non-Methyl HT-SELEX, 6 experiments	median	0.916	0.913	0.824	0.834	0.701	0.731
Non-Methyl HT-SELEX, 6 experiments	best	1.0	0.999	0.999	0.999	0.996	0.995

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.883	0.448	0.851	0.613
batch 2	0.819	0.759	0.781	0.611

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: 3.2.1.1.2
HGNC	HGNC:8621
MGI	MGI:97491
EntrezGene (human)	GeneID:5081 (SSTAR profile)
EntrezGene (mouse)	GeneID:18509 (SSTAR profile)
UniProt ID (human)	PAX7_HUMAN
UniProt ID (mouse)	PAX7_MOUSE
UniProt AC (human)	P23759 (TFClass)
UniProt AC (mouse)	P47239 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 3 mouse
HT-SELEX	6
Methyl-HT-SELEX	2

PCM	PAX7.H12INVIVO.1.S.B.pcm
PWM	PAX7.H12INVIVO.1.S.B.pwm
PFM	PAX7.H12INVIVO.1.S.B.pfm
Alignment	PAX7.H12INVIVO.1.S.B.words.tsv
Threshold to P-value map	PAX7.H12INVIVO.1.S.B.thr
Motif in other formats
JASPAR format	PAX7.H12INVIVO.1.S.B_jaspar_format.txt
MEME format	PAX7.H12INVIVO.1.S.B_meme_format.meme
Transfac format	PAX7.H12INVIVO.1.S.B_transfac_format.txt
Homer format	PAX7.H12INVIVO.1.S.B_homer_format_0.001.txt PAX7.H12INVIVO.1.S.B_homer_format_0.0005.txt PAX7.H12INVIVO.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2025.25	1779.25	2109.25	2476.25
02	1749.5	931.5	912.5	4796.5
03	7136.0	365.0	573.0	316.0
04	7380.0	309.0	335.0	366.0
05	113.0	359.0	266.0	7652.0
06	21.0	6701.0	83.0	1585.0
07	2006.0	29.0	6354.0	1.0
08	8385.0	0.0	5.0	0.0
09	0.0	0.0	0.0	8390.0
10	1.0	21.0	0.0	8368.0
11	8015.0	155.0	120.0	100.0
12	2419.0	1577.0	3678.0	716.0
13	594.75	3404.75	2122.75	2267.75
14	1719.0	2212.0	2518.0	1941.0

PFM

	A	C	G	T
01	0.241	0.212	0.251	0.295
02	0.209	0.111	0.109	0.572
03	0.851	0.044	0.068	0.038
04	0.88	0.037	0.04	0.044
05	0.013	0.043	0.032	0.912
06	0.003	0.799	0.01	0.189
07	0.239	0.003	0.757	0.0
08	0.999	0.0	0.001	0.0
09	0.0	0.0	0.0	1.0
10	0.0	0.003	0.0	0.997
11	0.955	0.018	0.014	0.012
12	0.288	0.188	0.438	0.085
13	0.071	0.406	0.253	0.27
14	0.205	0.264	0.3	0.231

PWM

	A	C	G	T
01	-0.035	-0.164	0.006	0.166
02	-0.181	-0.81	-0.831	0.827
03	1.224	-1.744	-1.295	-1.887
04	1.257	-1.909	-1.829	-1.741
05	-2.902	-1.76	-2.058	1.293
06	-4.503	1.161	-3.204	-0.28
07	-0.045	-4.207	1.108	-6.468
08	1.385	-6.835	-5.667	-6.835
09	-6.835	-6.835	-6.835	1.385
10	-6.468	-4.503	-6.835	1.383
11	1.34	-2.592	-2.843	-3.022
12	0.142	-0.285	0.561	-1.073
13	-1.258	0.484	0.012	0.078
14	-0.199	0.053	0.183	-0.077

Standard thresholds

P-value	Threshold
0.001	2.28826
0.0005	3.74236
0.0001	6.62596