USF1.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	USF1.H12RSNP.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	vGTCACGTGvbb
GC content	61.64%
Information content (bits; total / per base)	14.938 / 1.245
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	948

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	0.97	0.982	0.985	0.992	5.986	6.228	764.894	941.678
Mouse	5 (35)	0.987	0.99	0.965	0.978	0.983	0.988	5.744	6.065	840.553	917.174

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.999	0.998	0.999	0.998	0.995	0.992
Overall, 4 experiments	best	1.0	1.0	1.0	0.999	0.999	0.998
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	0.993	0.989
Non-Methyl HT-SELEX, 3 experiments	best	1.0	1.0	1.0	0.999	0.999	0.998

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	14.906	7.01	0.377	0.296

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.802	0.6	0.83	0.645

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.H12RSNP.0.PSM.A.pcm
PWM	USF1.H12RSNP.0.PSM.A.pwm
PFM	USF1.H12RSNP.0.PSM.A.pfm
Alignment	USF1.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	USF1.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	USF1.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	USF1.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	USF1.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	USF1.H12RSNP.0.PSM.A_homer_format_0.001.txt USF1.H12RSNP.0.PSM.A_homer_format_0.0005.txt USF1.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	253.0	146.0	430.0	119.0
02	95.0	9.0	844.0	0.0
03	14.0	17.0	14.0	903.0
04	0.0	947.0	1.0	0.0
05	947.0	1.0	0.0	0.0
06	1.0	908.0	8.0	31.0
07	180.0	16.0	751.0	1.0
08	7.0	6.0	2.0	933.0
09	0.0	0.0	947.0	1.0
10	382.0	138.0	388.0	40.0
11	50.0	448.0	232.0	218.0
12	84.0	478.0	281.0	105.0

PFM

	A	C	G	T
01	0.267	0.154	0.454	0.126
02	0.1	0.009	0.89	0.0
03	0.015	0.018	0.015	0.953
04	0.0	0.999	0.001	0.0
05	0.999	0.001	0.0	0.0
06	0.001	0.958	0.008	0.033
07	0.19	0.017	0.792	0.001
08	0.007	0.006	0.002	0.984
09	0.0	0.0	0.999	0.001
10	0.403	0.146	0.409	0.042
11	0.053	0.473	0.245	0.23
12	0.089	0.504	0.296	0.111

PWM

	A	C	G	T
01	0.065	-0.48	0.592	-0.682
02	-0.904	-3.104	1.265	-4.937
03	-2.721	-2.546	-2.721	1.332
04	-4.937	1.38	-4.477	-4.937
05	1.38	-4.477	-4.937	-4.937
06	-4.477	1.338	-3.202	-1.987
07	-0.273	-2.601	1.148	-4.477
08	-3.31	-3.432	-4.163	1.365
09	-4.937	-4.937	1.38	-4.477
10	0.475	-0.536	0.49	-1.744
11	-1.53	0.633	-0.021	-0.083
12	-1.024	0.698	0.169	-0.805

Standard thresholds

P-value	Threshold
0.001	2.194685
0.0005	3.63415
0.0001	6.40922