PAX7.H12INVITRO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX7.H12INVITRO.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	12
Consensus	dhdKTCAhRSYn
GC content	49.87%
Information content (bits; total / per base)	7.454 / 0.621
Data sources	ChIP-Seq
Aligned words	900

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)	0.755	0.801	0.626	0.666	0.708	0.765	2.11	2.42	95.456	158.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.55	0.549	0.526	0.52	0.511	0.512
Overall, 8 experiments	best	0.974	0.962	0.909	0.891	0.77	0.771
Methyl HT-SELEX, 2 experiments	median	0.808	0.798	0.729	0.728	0.634	0.651
Methyl HT-SELEX, 2 experiments	best	0.974	0.962	0.909	0.891	0.764	0.771
Non-Methyl HT-SELEX, 6 experiments	median	0.533	0.521	0.516	0.516	0.511	0.508
Non-Methyl HT-SELEX, 6 experiments	best	0.959	0.94	0.899	0.873	0.77	0.766

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.531	0.022	-0.058	-0.053
batch 2	0.556	0.366	0.114	0.039

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.H12INVITRO.0.P.B.pcm
PWM	PAX7.H12INVITRO.0.P.B.pwm
PFM	PAX7.H12INVITRO.0.P.B.pfm
Alignment	PAX7.H12INVITRO.0.P.B.words.tsv
Threshold to P-value map	PAX7.H12INVITRO.0.P.B.thr
Motif in other formats
JASPAR format	PAX7.H12INVITRO.0.P.B_jaspar_format.txt
MEME format	PAX7.H12INVITRO.0.P.B_meme_format.meme
Transfac format	PAX7.H12INVITRO.0.P.B_transfac_format.txt
Homer format	PAX7.H12INVITRO.0.P.B_homer_format_0.001.txt PAX7.H12INVITRO.0.P.B_homer_format_0.0005.txt PAX7.H12INVITRO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	179.0	125.0	180.0	416.0
02	200.0	156.0	104.0	440.0
03	206.0	82.0	266.0	346.0
04	13.0	31.0	647.0	209.0
05	32.0	139.0	20.0	709.0
06	21.0	796.0	3.0	80.0
07	748.0	96.0	3.0	53.0
08	127.0	425.0	50.0	298.0
09	202.0	23.0	605.0	70.0
10	14.0	357.0	516.0	13.0
11	122.0	155.0	54.0	569.0
12	118.0	247.0	306.0	229.0

PFM

	A	C	G	T
01	0.199	0.139	0.2	0.462
02	0.222	0.173	0.116	0.489
03	0.229	0.091	0.296	0.384
04	0.014	0.034	0.719	0.232
05	0.036	0.154	0.022	0.788
06	0.023	0.884	0.003	0.089
07	0.831	0.107	0.003	0.059
08	0.141	0.472	0.056	0.331
09	0.224	0.026	0.672	0.078
10	0.016	0.397	0.573	0.014
11	0.136	0.172	0.06	0.632
12	0.131	0.274	0.34	0.254

PWM

	A	C	G	T
01	-0.227	-0.582	-0.221	0.611
02	-0.117	-0.363	-0.763	0.667
03	-0.088	-0.996	0.166	0.428
04	-2.736	-1.936	1.051	-0.073
05	-1.906	-0.477	-2.346	1.143
06	-2.301	1.258	-3.876	-1.021
07	1.196	-0.842	-3.876	-1.422
08	-0.566	0.632	-1.478	0.279
09	-0.107	-2.217	0.984	-1.151
10	-2.67	0.459	0.826	-2.736
11	-0.606	-0.369	-1.404	0.923
12	-0.639	0.093	0.305	0.017

Standard thresholds

P-value	Threshold
0.001	5.053315
0.0005	5.69728
0.0001	6.979535