PAX7.H12INVITRO.2.PM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX7.H12INVITRO.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	nvnTAATTGATTWn
GC content	26.56%
Information content (bits; total / per base)	15.899 / 1.136
Data sources	ChIP-Seq + Methyl-HT-SELEX
Aligned words	9494

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)	0.684	0.976	0.534	0.97	0.535	0.968	1.432	7.128	49.745	971.523

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.999	0.997	0.986	0.983	0.86	0.872
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	0.938	0.934
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	0.913	0.912	0.822	0.833	0.698	0.728
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	0.875	0.366	0.797	0.576
batch 2	0.806	0.752	0.824	0.642

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.2.PM.A.pcm
PWM	PAX7.H12INVITRO.2.PM.A.pwm
PFM	PAX7.H12INVITRO.2.PM.A.pfm
Alignment	PAX7.H12INVITRO.2.PM.A.words.tsv
Threshold to P-value map	PAX7.H12INVITRO.2.PM.A.thr
Motif in other formats
JASPAR format	PAX7.H12INVITRO.2.PM.A_jaspar_format.txt
MEME format	PAX7.H12INVITRO.2.PM.A_meme_format.meme
Transfac format	PAX7.H12INVITRO.2.PM.A_transfac_format.txt
Homer format	PAX7.H12INVITRO.2.PM.A_homer_format_0.001.txt PAX7.H12INVITRO.2.PM.A_homer_format_0.0005.txt PAX7.H12INVITRO.2.PM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2299.0	2825.0	2216.0	2154.0
02	2308.0	2146.0	3821.0	1219.0
03	1388.0	2848.0	2395.0	2863.0
04	446.0	407.0	129.0	8512.0
05	9237.0	15.0	242.0	0.0
06	9494.0	0.0	0.0	0.0
07	0.0	1.0	1.0	9492.0
08	0.0	2549.0	35.0	6910.0
09	559.0	13.0	8922.0	0.0
10	9140.0	108.0	220.0	26.0
11	144.0	90.0	126.0	9134.0
12	163.0	237.0	175.0	8919.0
13	6822.75	489.75	701.75	1479.75
14	2753.25	2101.25	2487.25	2152.25

PFM

	A	C	G	T
01	0.242	0.298	0.233	0.227
02	0.243	0.226	0.402	0.128
03	0.146	0.3	0.252	0.302
04	0.047	0.043	0.014	0.897
05	0.973	0.002	0.025	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.268	0.004	0.728
09	0.059	0.001	0.94	0.0
10	0.963	0.011	0.023	0.003
11	0.015	0.009	0.013	0.962
12	0.017	0.025	0.018	0.939
13	0.719	0.052	0.074	0.156
14	0.29	0.221	0.262	0.227

PWM

	A	C	G	T
01	-0.032	0.174	-0.069	-0.097
02	-0.028	-0.101	0.476	-0.665
03	-0.536	0.182	0.009	0.187
04	-1.668	-1.759	-2.896	1.276
05	1.358	-4.923	-2.275	-6.945
06	1.386	-6.945	-6.945	-6.945
07	-6.945	-6.582	-6.582	1.385
08	-6.945	0.071	-4.154	1.068
09	-1.443	-5.046	1.323	-6.945
10	1.348	-3.07	-2.369	-4.431
11	-2.787	-3.248	-2.919	1.347
12	-2.665	-2.295	-2.595	1.323
13	1.055	-1.575	-1.216	-0.472
14	0.148	-0.122	0.047	-0.098

Standard thresholds

P-value	Threshold
0.001	1.21956
0.0005	2.77241
0.0001	5.95211