PAX7.H12RSNP.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX7.H12RSNP.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	15
Consensus	nnWAATCGATTAvbn
GC content	34.24%
Information content (bits; total / per base)	18.032 / 1.202
Data sources	HT-SELEX
Aligned words	9935

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)	0.698	0.979	0.557	0.974	0.549	0.97	1.448	6.34	41.337	991.097

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.998	0.997	0.986	0.983	0.859	0.871
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	0.988	0.985	0.935	0.932
Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.998	0.996	0.985	0.982
Non-Methyl HT-SELEX, 6 experiments	median	0.915	0.914	0.822	0.834	0.698	0.729
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	0.875	0.471	0.851	0.593
batch 2	0.819	0.764	0.842	0.659

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.1.S.B.pcm
PWM	PAX7.H12RSNP.1.S.B.pwm
PFM	PAX7.H12RSNP.1.S.B.pfm
Alignment	PAX7.H12RSNP.1.S.B.words.tsv
Threshold to P-value map	PAX7.H12RSNP.1.S.B.thr
Motif in other formats
JASPAR format	PAX7.H12RSNP.1.S.B_jaspar_format.txt
MEME format	PAX7.H12RSNP.1.S.B_meme_format.meme
Transfac format	PAX7.H12RSNP.1.S.B_transfac_format.txt
Homer format	PAX7.H12RSNP.1.S.B_homer_format_0.001.txt PAX7.H12RSNP.1.S.B_homer_format_0.0005.txt PAX7.H12RSNP.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2110.75	3160.75	2717.75	1945.75
02	2215.5	1555.5	3046.5	3117.5
03	1697.0	865.0	577.0	6796.0
04	9705.0	49.0	113.0	68.0
05	9798.0	34.0	10.0	93.0
06	8.0	52.0	30.0	9845.0
07	0.0	9381.0	3.0	551.0
08	773.0	6.0	9156.0	0.0
09	9933.0	1.0	1.0	0.0
10	0.0	0.0	0.0	9935.0
11	0.0	1.0	0.0	9934.0
12	9742.0	25.0	24.0	144.0
13	2034.0	2701.0	4685.0	515.0
14	562.0	4642.0	2416.0	2315.0
15	1873.5	2418.5	3359.5	2283.5

PFM

	A	C	G	T
01	0.212	0.318	0.274	0.196
02	0.223	0.157	0.307	0.314
03	0.171	0.087	0.058	0.684
04	0.977	0.005	0.011	0.007
05	0.986	0.003	0.001	0.009
06	0.001	0.005	0.003	0.991
07	0.0	0.944	0.0	0.055
08	0.078	0.001	0.922	0.0
09	1.0	0.0	0.0	0.0
10	0.0	0.0	0.0	1.0
11	0.0	0.0	0.0	1.0
12	0.981	0.003	0.002	0.014
13	0.205	0.272	0.472	0.052
14	0.057	0.467	0.243	0.233
15	0.189	0.243	0.338	0.23

PWM

	A	C	G	T
01	-0.163	0.241	0.09	-0.244
02	-0.114	-0.467	0.204	0.227
03	-0.38	-1.053	-1.457	1.006
04	1.362	-3.881	-3.071	-3.566
05	1.372	-4.227	-5.309	-3.261
06	-5.486	-3.824	-4.343	1.377
07	-6.985	1.328	-6.151	-1.503
08	-1.165	-5.702	1.304	-6.985
09	1.385	-6.624	-6.624	-6.985
10	-6.985	-6.985	-6.985	1.386
11	-6.985	-6.624	-6.985	1.385
12	1.366	-4.512	-4.549	-2.833
13	-0.2	0.084	0.634	-1.57
14	-1.483	0.625	-0.028	-0.07
15	-0.282	-0.027	0.302	-0.084

Standard thresholds

P-value	Threshold
0.001	-1.87154
0.0005	0.00021
0.0001	4.04251