PAX7.H12RSNP.2.PM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX7.H12RSNP.2.PM.A
Gene (human)	PAX7 (GeneCards)
Gene synonyms (human)	HUP1
Gene (mouse)	Pax7
Gene synonyms (mouse)	Pax-7
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	A

Motif length	14
Consensus	nWAATCAATTAnbn
GC content	26.03%
Information content (bits; total / per base)	17.103 / 1.222
Data sources	ChIP-Seq + Methyl-HT-SELEX
Aligned words	8399

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)	0.673	0.973	0.532	0.969	0.518	0.965	1.404	7.137	47.959	982.201

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.999	0.997	0.986	0.983	0.848	0.862
Overall, 8 experiments	best	0.999	0.998	0.999	0.998	0.996	0.995
Methyl HT-SELEX, 2 experiments	median	0.999	0.997	0.989	0.986	0.928	0.927
Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.998	0.997	0.985	0.983
Non-Methyl HT-SELEX, 6 experiments	median	0.909	0.91	0.819	0.831	0.693	0.724
Non-Methyl HT-SELEX, 6 experiments	best	0.999	0.998	0.999	0.998	0.996	0.995

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.861	0.429	0.79	0.549
batch 2	0.804	0.739	0.842	0.647

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.H12RSNP.2.PM.A.pcm
PWM	PAX7.H12RSNP.2.PM.A.pwm
PFM	PAX7.H12RSNP.2.PM.A.pfm
Alignment	PAX7.H12RSNP.2.PM.A.words.tsv
Threshold to P-value map	PAX7.H12RSNP.2.PM.A.thr
Motif in other formats
JASPAR format	PAX7.H12RSNP.2.PM.A_jaspar_format.txt
MEME format	PAX7.H12RSNP.2.PM.A_meme_format.meme
Transfac format	PAX7.H12RSNP.2.PM.A_transfac_format.txt
Homer format	PAX7.H12RSNP.2.PM.A_homer_format_0.001.txt PAX7.H12RSNP.2.PM.A_homer_format_0.0005.txt PAX7.H12RSNP.2.PM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1882.25	2263.25	1906.25	2347.25
02	1102.0	514.0	350.0	6433.0
03	8228.0	40.0	94.0	37.0
04	8380.0	5.0	6.0	8.0
05	0.0	32.0	5.0	8362.0
06	0.0	8188.0	1.0	210.0
07	6163.0	20.0	2216.0	0.0
08	8399.0	0.0	0.0	0.0
09	0.0	0.0	0.0	8399.0
10	0.0	130.0	8.0	8261.0
11	7633.0	96.0	294.0	376.0
12	2535.0	2143.0	2495.0	1226.0
13	1051.25	3428.25	1898.25	2021.25
14	1904.75	1975.75	2502.75	2015.75

PFM

	A	C	G	T
01	0.224	0.269	0.227	0.279
02	0.131	0.061	0.042	0.766
03	0.98	0.005	0.011	0.004
04	0.998	0.001	0.001	0.001
05	0.0	0.004	0.001	0.996
06	0.0	0.975	0.0	0.025
07	0.734	0.002	0.264	0.0
08	1.0	0.0	0.0	0.0
09	0.0	0.0	0.0	1.0
10	0.0	0.015	0.001	0.984
11	0.909	0.011	0.035	0.045
12	0.302	0.255	0.297	0.146
13	0.125	0.408	0.226	0.241
14	0.227	0.235	0.298	0.24

PWM

	A	C	G	T
01	-0.109	0.075	-0.097	0.111
02	-0.644	-1.404	-1.786	1.119
03	1.365	-3.907	-3.084	-3.98
04	1.383	-5.668	-5.539	-5.322
05	-6.836	-4.117	-5.668	1.381
06	-6.836	1.36	-6.469	-2.293
07	1.076	-4.548	0.054	-6.836
08	1.385	-6.836	-6.836	-6.836
09	-6.836	-6.836	-6.836	1.385
10	-6.836	-2.766	-5.322	1.369
11	1.29	-3.063	-1.959	-1.715
12	0.188	0.02	0.172	-0.537
13	-0.691	0.49	-0.101	-0.038
14	-0.097	-0.061	0.175	-0.041

Standard thresholds

P-value	Threshold
0.001	-1.05924
0.0005	0.86521
0.0001	4.69158