CUX1.H12RSNP.2.P.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CUX1.H12RSNP.2.P.C
Gene (human)	CUX1 (GeneCards)
Gene synonyms (human)	CUTL1
Gene (mouse)	Cux1
Gene synonyms (mouse)	Cutl1, Cux, Kiaa4047
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	C

Motif length	19
Consensus	WWdATKGWKKndYWbWKKh
GC content	41.87%
Information content (bits; total / per base)	12.274 / 0.646
Data sources	ChIP-Seq
Aligned words	1000

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	5 (32)	0.601	0.826	0.42	0.801	0.572	0.801	1.258	7.812	5.115	112.0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.608	0.56	0.593	0.555	0.571	0.545
Overall, 4 experiments	best	0.635	0.576	0.626	0.573	0.605	0.564
Methyl HT-SELEX, 1 experiments	median	0.62	0.567	0.603	0.561	0.579	0.55
Methyl HT-SELEX, 1 experiments	best	0.62	0.567	0.603	0.561	0.579	0.55
Non-Methyl HT-SELEX, 3 experiments	median	0.596	0.554	0.584	0.549	0.562	0.539
Non-Methyl HT-SELEX, 3 experiments	best	0.635	0.576	0.626	0.573	0.605	0.564

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.574	0.137	0.345	0.207
batch 2	0.575	0.178	0.337	0.212

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HD-CUT {3.1.9} (TFClass)
TF subfamily	CUX {3.1.9.2} (TFClass)
TFClass ID	TFClass: 3.1.9.2.1
HGNC	HGNC:2557
MGI	MGI:88568
EntrezGene (human)	GeneID:1523 (SSTAR profile)
EntrezGene (mouse)	GeneID:13047 (SSTAR profile)
UniProt ID (human)	CUX1_HUMAN
UniProt ID (mouse)	CUX1_MOUSE
UniProt AC (human)	P39880 (TFClass)
UniProt AC (mouse)	P53564 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	CUX1.H12RSNP.2.P.C.pcm
PWM	CUX1.H12RSNP.2.P.C.pwm
PFM	CUX1.H12RSNP.2.P.C.pfm
Alignment	CUX1.H12RSNP.2.P.C.words.tsv
Threshold to P-value map	CUX1.H12RSNP.2.P.C.thr
Motif in other formats
JASPAR format	CUX1.H12RSNP.2.P.C_jaspar_format.txt
MEME format	CUX1.H12RSNP.2.P.C_meme_format.meme
Transfac format	CUX1.H12RSNP.2.P.C_transfac_format.txt
Homer format	CUX1.H12RSNP.2.P.C_homer_format_0.001.txt CUX1.H12RSNP.2.P.C_homer_format_0.0005.txt CUX1.H12RSNP.2.P.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	676.0	111.0	58.0	155.0
02	722.0	22.0	53.0	203.0
03	163.0	130.0	575.0	132.0
04	871.0	88.0	23.0	18.0
05	85.0	11.0	97.0	807.0
06	57.0	16.0	674.0	253.0
07	58.0	88.0	834.0	20.0
08	805.0	73.0	47.0	75.0
09	58.0	39.0	594.0	309.0
10	104.0	77.0	138.0	681.0
11	135.0	287.0	239.0	339.0
12	462.0	61.0	388.0	89.0
13	47.0	580.0	132.0	241.0
14	208.0	77.0	29.0	686.0
15	95.0	437.0	265.0	203.0
16	328.0	58.0	54.0	560.0
17	68.0	28.0	509.0	395.0
18	103.0	38.0	732.0	127.0
19	147.0	173.0	121.0	559.0

PFM

	A	C	G	T
01	0.676	0.111	0.058	0.155
02	0.722	0.022	0.053	0.203
03	0.163	0.13	0.575	0.132
04	0.871	0.088	0.023	0.018
05	0.085	0.011	0.097	0.807
06	0.057	0.016	0.674	0.253
07	0.058	0.088	0.834	0.02
08	0.805	0.073	0.047	0.075
09	0.058	0.039	0.594	0.309
10	0.104	0.077	0.138	0.681
11	0.135	0.287	0.239	0.339
12	0.462	0.061	0.388	0.089
13	0.047	0.58	0.132	0.241
14	0.208	0.077	0.029	0.686
15	0.095	0.437	0.265	0.203
16	0.328	0.058	0.054	0.56
17	0.068	0.028	0.509	0.395
18	0.103	0.038	0.732	0.127
19	0.147	0.173	0.121	0.559

PWM

	A	C	G	T
01	0.99	-0.803	-1.439	-0.474
02	1.056	-2.362	-1.526	-0.207
03	-0.424	-0.648	0.829	-0.633
04	1.243	-1.032	-2.32	-2.546
05	-1.066	-2.985	-0.936	1.167
06	-1.455	-2.653	0.987	0.012
07	-1.439	-1.032	1.2	-2.45
08	1.165	-1.215	-1.642	-1.188
09	-1.439	-1.821	0.861	0.211
10	-0.867	-1.162	-0.589	0.998
11	-0.61	0.137	-0.045	0.303
12	0.611	-1.39	0.437	-1.02
13	-1.642	0.838	-0.633	-0.036
14	-0.183	-1.162	-2.103	1.005
15	-0.956	0.556	0.058	-0.207
16	0.27	-1.439	-1.508	0.803
17	-1.284	-2.136	0.707	0.455
18	-0.877	-1.846	1.07	-0.671
19	-0.526	-0.365	-0.718	0.801

Standard thresholds

P-value	Threshold
0.001	4.21056
0.0005	5.09936
0.0001	6.98061