USF1.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	USF1.H12INVITRO.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	13
Consensus	nnvGTCACGTGdb
GC content	54.47%
Information content (bits; total / per base)	14.176 / 1.09
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9933

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)	0.986	0.992	0.965	0.981	0.984	0.99	5.932	6.191	740.581	910.854
Mouse	5 (35)	0.986	0.991	0.965	0.975	0.986	0.99	5.886	6.184	824.244	904.032

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

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	7.096	4.991	0.332	0.278

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.812	0.605	0.827	0.648

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.H12INVITRO.0.PSM.A.pcm
PWM	USF1.H12INVITRO.0.PSM.A.pwm
PFM	USF1.H12INVITRO.0.PSM.A.pfm
Alignment	USF1.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	USF1.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	USF1.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	USF1.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	USF1.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	USF1.H12INVITRO.0.PSM.A_homer_format_0.001.txt USF1.H12INVITRO.0.PSM.A_homer_format_0.0005.txt USF1.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2303.75	2729.75	2879.75	2019.75
02	3261.25	1288.25	2804.25	2579.25
03	1860.0	1993.0	4739.0	1341.0
04	2264.0	82.0	7563.0	24.0
05	56.0	197.0	201.0	9479.0
06	1.0	9924.0	8.0	0.0
07	9933.0	0.0	0.0	0.0
08	0.0	9259.0	198.0	476.0
09	2110.0	52.0	7771.0	0.0
10	19.0	90.0	10.0	9814.0
11	4.0	4.0	9866.0	59.0
12	4790.5	986.5	2868.5	1287.5
13	704.75	2903.75	1919.75	4404.75

PFM

	A	C	G	T
01	0.232	0.275	0.29	0.203
02	0.328	0.13	0.282	0.26
03	0.187	0.201	0.477	0.135
04	0.228	0.008	0.761	0.002
05	0.006	0.02	0.02	0.954
06	0.0	0.999	0.001	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.932	0.02	0.048
09	0.212	0.005	0.782	0.0
10	0.002	0.009	0.001	0.988
11	0.0	0.0	0.993	0.006
12	0.482	0.099	0.289	0.13
13	0.071	0.292	0.193	0.443

PWM

	A	C	G	T
01	-0.075	0.095	0.148	-0.206
02	0.272	-0.655	0.121	0.038
03	-0.289	-0.22	0.646	-0.615
04	-0.092	-3.384	1.113	-4.549
05	-3.753	-2.523	-2.504	1.339
06	-6.624	1.385	-5.486	-6.985
07	1.386	-6.985	-6.985	-6.985
08	-6.985	1.315	-2.518	-1.648
09	-0.163	-3.824	1.14	-6.985
10	-4.76	-3.293	-5.309	1.374
11	-5.978	-5.978	1.379	-3.702
12	0.657	-0.922	0.144	-0.656
13	-1.257	0.156	-0.257	0.573

Standard thresholds

P-value	Threshold
0.001	1.87886
0.0005	3.48321
0.0001	6.541735