USF2.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	USF2.H12INVIVO.0.PSM.A
Gene (human)	USF2 (GeneCards)
Gene synonyms (human)	BHLHB12
Gene (mouse)	Usf2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	18
Consensus	nvdGTCACGTGvbvnbnv
GC content	62.83%
Information content (bits; total / per base)	15.762 / 0.876
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	930

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	14 (93)	0.984	0.995	0.967	0.988	0.98	0.994	6.151	6.995	708.62	843.959
Mouse	5 (33)	0.968	0.992	0.942	0.973	0.964	0.993	5.762	6.461	530.721	882.854

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.999	0.997	0.996	0.994	0.945	0.948
Overall, 4 experiments	best	0.999	0.998	0.998	0.996	0.997	0.995
Methyl HT-SELEX, 2 experiments	median	0.998	0.997	0.996	0.994	0.945	0.948
Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.998	0.996	0.997	0.995
Non-Methyl HT-SELEX, 2 experiments	median	0.999	0.997	0.952	0.955	0.86	0.877
Non-Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.998	0.996	0.996	0.994

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.386	3.337	0.17	0.11

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.909	0.593	0.842	0.612

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: 1.2.6.2.2
HGNC	HGNC:12594
MGI	MGI:99961
EntrezGene (human)	GeneID:7392 (SSTAR profile)
EntrezGene (mouse)	GeneID:22282 (SSTAR profile)
UniProt ID (human)	USF2_HUMAN
UniProt ID (mouse)	USF2_MOUSE
UniProt AC (human)	Q15853 (TFClass)
UniProt AC (mouse)	Q64705 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	14 human, 5 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	USF2.H12INVIVO.0.PSM.A.pcm
PWM	USF2.H12INVIVO.0.PSM.A.pwm
PFM	USF2.H12INVIVO.0.PSM.A.pfm
Alignment	USF2.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	USF2.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	USF2.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	USF2.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	USF2.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	USF2.H12INVIVO.0.PSM.A_homer_format_0.001.txt USF2.H12INVIVO.0.PSM.A_homer_format_0.0005.txt USF2.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	137.0	308.0	280.0	205.0
02	178.0	246.0	375.0	131.0
03	254.0	114.0	438.0	124.0
04	107.0	13.0	810.0	0.0
05	9.0	20.0	13.0	888.0
06	0.0	930.0	0.0	0.0
07	927.0	1.0	0.0	2.0
08	0.0	903.0	10.0	17.0
09	123.0	0.0	807.0	0.0
10	1.0	3.0	1.0	925.0
11	0.0	0.0	929.0	1.0
12	383.0	123.0	341.0	83.0
13	48.0	408.0	233.0	241.0
14	98.0	435.0	323.0	74.0
15	254.0	283.0	281.0	112.0
16	135.0	303.0	345.0	147.0
17	187.0	250.0	351.0	142.0
18	149.0	288.0	352.0	141.0

PFM

	A	C	G	T
01	0.147	0.331	0.301	0.22
02	0.191	0.265	0.403	0.141
03	0.273	0.123	0.471	0.133
04	0.115	0.014	0.871	0.0
05	0.01	0.022	0.014	0.955
06	0.0	1.0	0.0	0.0
07	0.997	0.001	0.0	0.002
08	0.0	0.971	0.011	0.018
09	0.132	0.0	0.868	0.0
10	0.001	0.003	0.001	0.995
11	0.0	0.0	0.999	0.001
12	0.412	0.132	0.367	0.089
13	0.052	0.439	0.251	0.259
14	0.105	0.468	0.347	0.08
15	0.273	0.304	0.302	0.12
16	0.145	0.326	0.371	0.158
17	0.201	0.269	0.377	0.153
18	0.16	0.31	0.378	0.152

PWM

	A	C	G	T
01	-0.524	0.279	0.185	-0.125
02	-0.265	0.056	0.475	-0.568
03	0.088	-0.705	0.63	-0.622
04	-0.768	-2.768	1.243	-4.92
05	-3.085	-2.378	-2.768	1.335
06	-4.92	1.381	-4.92	-4.92
07	1.378	-4.46	-4.92	-4.146
08	-4.92	1.351	-2.996	-2.527
09	-0.63	-4.92	1.239	-4.92
10	-4.46	-3.907	-4.46	1.375
11	-4.92	-4.92	1.38	-4.46
12	0.496	-0.63	0.381	-1.017
13	-1.55	0.559	0.002	0.036
14	-0.854	0.623	0.327	-1.129
15	0.088	0.195	0.188	-0.723
16	-0.538	0.263	0.392	-0.454
17	-0.216	0.072	0.409	-0.488
18	-0.441	0.213	0.412	-0.495

Standard thresholds

P-value	Threshold
0.001	1.63846
0.0005	3.14456
0.0001	6.06696