PAX7.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX7.H12INVIVO.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	hdhdGYCAYRSYb
GC content	47.24%
Information content (bits; total / per base)	9.163 / 0.705
Data sources	ChIP-Seq
Aligned words	994

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)	0.752	0.793	0.617	0.675	0.709	0.757	2.046	2.305	90.131	163.143

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.544	0.543	0.531	0.519	0.516	0.514
Overall, 8 experiments	best	0.965	0.951	0.891	0.871	0.758	0.759
Methyl HT-SELEX, 2 experiments	median	0.798	0.787	0.724	0.717	0.636	0.646
Methyl HT-SELEX, 2 experiments	best	0.965	0.951	0.891	0.871	0.758	0.759
Non-Methyl HT-SELEX, 6 experiments	median	0.542	0.525	0.522	0.517	0.513	0.51
Non-Methyl HT-SELEX, 6 experiments	best	0.944	0.92	0.879	0.848	0.758	0.749

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.54	0.02	0.048	0.007
batch 2	0.496	0.322	0.189	0.124

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.0.P.B.pcm
PWM	PAX7.H12INVIVO.0.P.B.pwm
PFM	PAX7.H12INVIVO.0.P.B.pfm
Alignment	PAX7.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	PAX7.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	PAX7.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	PAX7.H12INVIVO.0.P.B_meme_format.meme
Transfac format	PAX7.H12INVIVO.0.P.B_transfac_format.txt
Homer format	PAX7.H12INVIVO.0.P.B_homer_format_0.001.txt PAX7.H12INVIVO.0.P.B_homer_format_0.0005.txt PAX7.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	435.0	232.0	139.0	188.0
02	263.0	144.0	154.0	433.0
03	215.0	216.0	69.0	494.0
04	284.0	46.0	186.0	478.0
05	5.0	5.0	695.0	289.0
06	45.0	220.0	60.0	669.0
07	8.0	972.0	4.0	10.0
08	949.0	10.0	6.0	29.0
09	67.0	573.0	22.0	332.0
10	323.0	8.0	630.0	33.0
11	7.0	393.0	590.0	4.0
12	127.0	239.0	26.0	602.0
13	133.0	246.0	219.0	396.0

PFM

	A	C	G	T
01	0.438	0.233	0.14	0.189
02	0.265	0.145	0.155	0.436
03	0.216	0.217	0.069	0.497
04	0.286	0.046	0.187	0.481
05	0.005	0.005	0.699	0.291
06	0.045	0.221	0.06	0.673
07	0.008	0.978	0.004	0.01
08	0.955	0.01	0.006	0.029
09	0.067	0.576	0.022	0.334
10	0.325	0.008	0.634	0.033
11	0.007	0.395	0.594	0.004
12	0.128	0.24	0.026	0.606
13	0.134	0.247	0.22	0.398

PWM

	A	C	G	T
01	0.557	-0.068	-0.576	-0.277
02	0.056	-0.541	-0.474	0.552
03	-0.144	-0.139	-1.264	0.684
04	0.133	-1.657	-0.287	0.651
05	-3.616	-3.616	1.024	0.15
06	-1.678	-0.121	-1.4	0.986
07	-3.248	1.359	-3.777	-3.061
08	1.335	-3.061	-3.478	-2.097
09	-1.292	0.832	-2.356	0.288
10	0.261	-3.248	0.926	-1.975
11	-3.356	0.456	0.861	-3.777
12	-0.665	-0.039	-2.2	0.881
13	-0.619	-0.01	-0.125	0.463

Standard thresholds

P-value	Threshold
0.001	5.01671
0.0005	5.83961
0.0001	7.33726