PAX7.H12INVITRO.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX7.H12INVITRO.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	nWAATCGATTAvbn
GC content	30.12%
Information content (bits; total / per base)	16.477 / 1.177
Data sources	HT-SELEX
Aligned words	6971

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)	0.694	0.979	0.547	0.973	0.55	0.972	1.447	6.626	47.602	976.125

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.998	0.997	0.987	0.984	0.864	0.875
Overall, 8 experiments	best	1.0	0.999	0.999	0.999	0.997	0.996
Methyl HT-SELEX, 2 experiments	median	0.998	0.997	0.989	0.986	0.94	0.937
Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.998	0.997	0.986	0.983
Non-Methyl HT-SELEX, 6 experiments	median	0.916	0.914	0.824	0.835	0.699	0.73
Non-Methyl HT-SELEX, 6 experiments	best	1.0	0.999	0.999	0.999	0.997	0.996

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.876	0.508	0.85	0.586
batch 2	0.806	0.753	0.834	0.66

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.1.S.B.pcm
PWM	PAX7.H12INVITRO.1.S.B.pwm
PFM	PAX7.H12INVITRO.1.S.B.pfm
Alignment	PAX7.H12INVITRO.1.S.B.words.tsv
Threshold to P-value map	PAX7.H12INVITRO.1.S.B.thr
Motif in other formats
JASPAR format	PAX7.H12INVITRO.1.S.B_jaspar_format.txt
MEME format	PAX7.H12INVITRO.1.S.B_meme_format.meme
Transfac format	PAX7.H12INVITRO.1.S.B_transfac_format.txt
Homer format	PAX7.H12INVITRO.1.S.B_homer_format_0.001.txt PAX7.H12INVITRO.1.S.B_homer_format_0.0005.txt PAX7.H12INVITRO.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1657.0	1416.0	1835.0	2063.0
02	1331.25	625.25	654.25	4360.25
03	6580.0	95.0	202.0	94.0
04	6794.0	37.0	37.0	103.0
05	8.0	89.0	25.0	6849.0
06	1.0	5872.0	25.0	1073.0
07	1537.0	12.0	5422.0	0.0
08	6968.0	0.0	3.0	0.0
09	0.0	0.0	0.0	6971.0
10	0.0	5.0	0.0	6966.0
11	6752.0	102.0	59.0	58.0
12	2044.0	1321.0	3004.0	602.0
13	444.25	2881.25	1782.25	1863.25
14	1439.25	1806.25	2085.25	1640.25

PFM

	A	C	G	T
01	0.238	0.203	0.263	0.296
02	0.191	0.09	0.094	0.625
03	0.944	0.014	0.029	0.013
04	0.975	0.005	0.005	0.015
05	0.001	0.013	0.004	0.982
06	0.0	0.842	0.004	0.154
07	0.22	0.002	0.778	0.0
08	1.0	0.0	0.0	0.0
09	0.0	0.0	0.0	1.0
10	0.0	0.001	0.0	0.999
11	0.969	0.015	0.008	0.008
12	0.293	0.189	0.431	0.086
13	0.064	0.413	0.256	0.267
14	0.206	0.259	0.299	0.235

PWM

	A	C	G	T
01	-0.05	-0.207	0.052	0.169
02	-0.269	-1.023	-0.978	0.916
03	1.328	-2.888	-2.145	-2.898
04	1.36	-3.795	-3.795	-2.809
05	-5.141	-2.951	-4.161	1.368
06	-6.297	1.214	-4.161	-0.484
07	-0.125	-4.81	1.134	-6.67
08	1.385	-6.67	-5.813	-6.67
09	-6.67	-6.67	-6.67	1.385
10	-6.67	-5.489	-6.67	1.385
11	1.353	-2.818	-3.35	-3.367
12	0.159	-0.277	0.544	-1.061
13	-1.363	0.502	0.022	0.067
14	-0.191	0.036	0.179	-0.061

Standard thresholds

P-value	Threshold
0.001	0.18476
0.0005	1.85861
0.0001	5.455365