USF1.H12CORE.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	USF1.H12CORE.0.PSM.A
Gene (human)	USF1 (GeneCards)
Gene synonyms (human)	BHLHB11, USF
Gene (mouse)	Usf1
Gene synonyms (mouse)	Usf
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	dGTCACGTGvbv
GC content	60.3%
Information content (bits; total / per base)	14.815 / 1.235
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	911

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
Human	16 (110)	0.988	0.993	0.971	0.982	0.986	0.992	6.009	6.245	763.502	946.921
Mouse	5 (35)	0.988	0.991	0.967	0.979	0.986	0.989	5.885	6.155	836.538	923.553

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.999	0.998	0.999	0.998	0.996	0.993
Overall, 4 experiments	best	1.0	1.0	1.0	0.999	0.999	0.999
Methyl HT-SELEX, 1 experiments	median	0.999	0.997	0.998	0.996	0.997	0.995
Methyl HT-SELEX, 1 experiments	best	0.999	0.997	0.998	0.996	0.997	0.995
Non-Methyl HT-SELEX, 3 experiments	median	1.0	0.999	0.999	0.999	0.994	0.991
Non-Methyl HT-SELEX, 3 experiments	best	1.0	1.0	1.0	0.999	0.999	0.999

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	8.615	5.479	0.345	0.272

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.806	0.625	0.836	0.654

TF superclass	Basic domains {1} (TFClass)
TF class	Basic helix-loop-helix factors (bHLH) {1.2} (TFClass)
TF family	bHLH-ZIP {1.2.6} (TFClass)
TF subfamily	USF {1.2.6.2} (TFClass)
TFClass ID	TFClass: 1.2.6.2.1
HGNC	HGNC:12593
MGI	MGI:99542
EntrezGene (human)	GeneID:7391 (SSTAR profile)
EntrezGene (mouse)	GeneID:22278 (SSTAR profile)
UniProt ID (human)	USF1_HUMAN
UniProt ID (mouse)	USF1_MOUSE
UniProt AC (human)	P22415 (TFClass)
UniProt AC (mouse)	Q61069 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	16 human, 5 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	USF1.H12CORE.0.PSM.A.pcm
PWM	USF1.H12CORE.0.PSM.A.pwm
PFM	USF1.H12CORE.0.PSM.A.pfm
Alignment	USF1.H12CORE.0.PSM.A.words.tsv
Threshold to P-value map	USF1.H12CORE.0.PSM.A.thr
Motif in other formats
JASPAR format	USF1.H12CORE.0.PSM.A_jaspar_format.txt
MEME format	USF1.H12CORE.0.PSM.A_meme_format.meme
Transfac format	USF1.H12CORE.0.PSM.A_transfac_format.txt
Homer format	USF1.H12CORE.0.PSM.A_homer_format_0.001.txt USF1.H12CORE.0.PSM.A_homer_format_0.0005.txt USF1.H12CORE.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	258.0	103.0	413.0	137.0
02	123.0	14.0	768.0	6.0
03	13.0	22.0	13.0	863.0
04	0.0	911.0	0.0	0.0
05	909.0	0.0	0.0	2.0
06	0.0	880.0	11.0	20.0
07	138.0	3.0	770.0	0.0
08	3.0	1.0	2.0	905.0
09	0.0	0.0	911.0	0.0
10	339.0	114.0	373.0	85.0
11	57.0	346.0	222.0	286.0
12	109.0	415.0	300.0	87.0

PFM

	A	C	G	T
01	0.283	0.113	0.453	0.15
02	0.135	0.015	0.843	0.007
03	0.014	0.024	0.014	0.947
04	0.0	1.0	0.0	0.0
05	0.998	0.0	0.0	0.002
06	0.0	0.966	0.012	0.022
07	0.151	0.003	0.845	0.0
08	0.003	0.001	0.002	0.993
09	0.0	0.0	1.0	0.0
10	0.372	0.125	0.409	0.093
11	0.063	0.38	0.244	0.314
12	0.12	0.456	0.329	0.095

PWM

	A	C	G	T
01	0.124	-0.785	0.592	-0.503
02	-0.61	-2.682	1.21	-3.394
03	-2.748	-2.27	-2.748	1.327
04	-4.903	1.381	-4.903	-4.903
05	1.379	-4.903	-4.903	-4.126
06	-4.903	1.346	-2.894	-2.358
07	-0.496	-3.887	1.213	-4.903
08	-3.887	-4.441	-4.126	1.374
09	-4.903	-4.903	1.381	-4.903
10	0.395	-0.685	0.49	-0.973
11	-1.363	0.416	-0.025	0.226
12	-0.729	0.597	0.274	-0.95

Standard thresholds

P-value	Threshold
0.001	2.172745
0.0005	3.655225
0.0001	6.41324