CUX2.H12RSNP.0.P.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CUX2.H12RSNP.0.P.C
Gene (human)	CUX2 (GeneCards)
Gene synonyms (human)	CUTL2, KIAA0293
Gene (mouse)	Cux2
Gene synonyms (mouse)	Cutl2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	C

Motif length	11
Consensus	hnbATTGATYd
GC content	26.65%
Information content (bits; total / per base)	11.452 / 1.041
Data sources	ChIP-Seq
Aligned words	955

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
Mouse	1 (5)	0.848	0.885	0.788	0.827	0.826	0.86	3.13	3.394	205.796	254.745

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.938	0.898	0.847	0.821	0.675	0.698
Overall, 4 experiments	best	0.95	0.911	0.94	0.9	0.894	0.857
Methyl HT-SELEX, 1 experiments	median	0.936	0.89	0.852	0.822	0.68	0.701
Methyl HT-SELEX, 1 experiments	best	0.936	0.89	0.852	0.822	0.68	0.701
Non-Methyl HT-SELEX, 3 experiments	median	0.941	0.906	0.842	0.82	0.67	0.696
Non-Methyl HT-SELEX, 3 experiments	best	0.95	0.911	0.94	0.9	0.894	0.857

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.884	0.634	0.839	0.572

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: 3.1.9.2.2
HGNC	HGNC:19347
MGI	MGI:107321
EntrezGene (human)	GeneID:23316 (SSTAR profile)
EntrezGene (mouse)	GeneID:13048 (SSTAR profile)
UniProt ID (human)	CUX2_HUMAN
UniProt ID (mouse)	CUX2_MOUSE
UniProt AC (human)	O14529 (TFClass)
UniProt AC (mouse)	P70298 (TFClass)
GRECO-DB-TF	yes

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

PCM	CUX2.H12RSNP.0.P.C.pcm
PWM	CUX2.H12RSNP.0.P.C.pwm
PFM	CUX2.H12RSNP.0.P.C.pfm
Alignment	CUX2.H12RSNP.0.P.C.words.tsv
Threshold to P-value map	CUX2.H12RSNP.0.P.C.thr
Motif in other formats
JASPAR format	CUX2.H12RSNP.0.P.C_jaspar_format.txt
MEME format	CUX2.H12RSNP.0.P.C_meme_format.meme
Transfac format	CUX2.H12RSNP.0.P.C_transfac_format.txt
Homer format	CUX2.H12RSNP.0.P.C_homer_format_0.001.txt CUX2.H12RSNP.0.P.C_homer_format_0.0005.txt CUX2.H12RSNP.0.P.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	190.0	152.0	138.0	475.0
02	130.0	174.0	130.0	521.0
03	76.0	208.0	219.0	452.0
04	907.0	17.0	12.0	19.0
05	25.0	5.0	53.0	872.0
06	13.0	62.0	20.0	860.0
07	3.0	5.0	940.0	7.0
08	926.0	11.0	5.0	13.0
09	22.0	52.0	9.0	872.0
10	14.0	238.0	18.0	685.0
11	212.0	95.0	237.0	411.0

PFM

	A	C	G	T
01	0.199	0.159	0.145	0.497
02	0.136	0.182	0.136	0.546
03	0.08	0.218	0.229	0.473
04	0.95	0.018	0.013	0.02
05	0.026	0.005	0.055	0.913
06	0.014	0.065	0.021	0.901
07	0.003	0.005	0.984	0.007
08	0.97	0.012	0.005	0.014
09	0.023	0.054	0.009	0.913
10	0.015	0.249	0.019	0.717
11	0.222	0.099	0.248	0.43

PWM

	A	C	G	T
01	-0.227	-0.447	-0.543	0.684
02	-0.602	-0.314	-0.602	0.776
03	-1.13	-0.137	-0.086	0.635
04	1.329	-2.553	-2.864	-2.452
05	-2.197	-3.578	-1.48	1.29
06	-2.794	-1.328	-2.405	1.276
07	-3.932	-3.578	1.365	-3.317
08	1.35	-2.94	-3.578	-2.794
09	-2.316	-1.499	-3.111	1.29
10	-2.728	-0.003	-2.501	1.049
11	-0.118	-0.911	-0.007	0.54

Standard thresholds

P-value	Threshold
0.001	4.34812
0.0005	5.264755
0.0001	7.25792