PAX7.H12RSNP.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX7.H12RSNP.0.P.B
Gene (human)	PAX7 (GeneCards)
Gene synonyms (human)	HUP1
Gene (mouse)	Pax7
Gene synonyms (mouse)	Pax-7
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	13
Consensus	hdhdKYCAYRSYn
GC content	47.75%
Information content (bits; total / per base)	7.285 / 0.56
Data sources	ChIP-Seq
Aligned words	825

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)	0.751	0.787	0.617	0.669	0.702	0.746	1.983	2.228	76.119	142.027

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.549	0.546	0.532	0.52	0.515	0.515
Overall, 8 experiments	best	0.963	0.948	0.887	0.866	0.75	0.753
Methyl HT-SELEX, 2 experiments	median	0.799	0.787	0.717	0.714	0.627	0.641
Methyl HT-SELEX, 2 experiments	best	0.963	0.948	0.887	0.866	0.75	0.753
Non-Methyl HT-SELEX, 6 experiments	median	0.541	0.524	0.523	0.518	0.515	0.51
Non-Methyl HT-SELEX, 6 experiments	best	0.939	0.913	0.868	0.837	0.75	0.741

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.543	0.019	0.053	0.031
batch 2	0.537	0.34	0.179	0.078

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.0.P.B.pcm
PWM	PAX7.H12RSNP.0.P.B.pwm
PFM	PAX7.H12RSNP.0.P.B.pfm
Alignment	PAX7.H12RSNP.0.P.B.words.tsv
Threshold to P-value map	PAX7.H12RSNP.0.P.B.thr
Motif in other formats
JASPAR format	PAX7.H12RSNP.0.P.B_jaspar_format.txt
MEME format	PAX7.H12RSNP.0.P.B_meme_format.meme
Transfac format	PAX7.H12RSNP.0.P.B_transfac_format.txt
Homer format	PAX7.H12RSNP.0.P.B_homer_format_0.001.txt PAX7.H12RSNP.0.P.B_homer_format_0.0005.txt PAX7.H12RSNP.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	363.0	189.0	106.0	167.0
02	171.0	117.0	159.0	378.0
03	172.0	183.0	69.0	401.0
04	223.0	47.0	131.0	424.0
05	13.0	10.0	538.0	264.0
06	43.0	211.0	59.0	512.0
07	2.0	745.0	6.0	72.0
08	687.0	100.0	5.0	33.0
09	59.0	453.0	38.0	275.0
10	233.0	38.0	475.0	79.0
11	20.0	383.0	389.0	33.0
12	125.0	181.0	26.0	493.0
13	100.0	238.0	225.0	262.0

PFM

	A	C	G	T
01	0.44	0.229	0.128	0.202
02	0.207	0.142	0.193	0.458
03	0.208	0.222	0.084	0.486
04	0.27	0.057	0.159	0.514
05	0.016	0.012	0.652	0.32
06	0.052	0.256	0.072	0.621
07	0.002	0.903	0.007	0.087
08	0.833	0.121	0.006	0.04
09	0.072	0.549	0.046	0.333
10	0.282	0.046	0.576	0.096
11	0.024	0.464	0.472	0.04
12	0.152	0.219	0.032	0.598
13	0.121	0.288	0.273	0.318

PWM

	A	C	G	T
01	0.562	-0.087	-0.658	-0.209
02	-0.186	-0.561	-0.258	0.602
03	-0.18	-0.119	-1.079	0.661
04	0.077	-1.452	-0.449	0.716
05	-2.651	-2.879	0.954	0.245
06	-1.538	0.023	-1.232	0.904
07	-4.035	1.278	-3.299	-1.037
08	1.198	-0.715	-3.438	-1.791
09	-1.232	0.782	-1.656	0.286
10	0.121	-1.656	0.83	-0.947
11	-2.261	0.615	0.631	-1.791
12	-0.496	-0.129	-2.017	0.867
13	-0.715	0.142	0.086	0.238

Standard thresholds

P-value	Threshold
0.001	5.06816
0.0005	5.69091
0.0001	6.91982