CUX2.H12RSNP.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CUX2.H12RSNP.1.SM.B
Gene (human)	CUX2 (GeneCards)
Gene synonyms (human)	CUTL2, KIAA0293
Gene (mouse)	Cux2
Gene synonyms (mouse)	Cutl2
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	13
Consensus	ndTATCGATYMnn
GC content	33.36%
Information content (bits; total / per base)	14.911 / 1.147
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	7035

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)	0.837	0.87	0.797	0.828	0.805	0.839	2.755	3.011	180.114	230.585

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.982	0.97	0.882	0.883	0.694	0.734
Overall, 4 experiments	best	0.991	0.986	0.968	0.95	0.912	0.892
Methyl HT-SELEX, 1 experiments	median	0.984	0.973	0.882	0.877	0.701	0.735
Methyl HT-SELEX, 1 experiments	best	0.984	0.973	0.882	0.877	0.701	0.735
Non-Methyl HT-SELEX, 3 experiments	median	0.981	0.967	0.883	0.888	0.688	0.733
Non-Methyl HT-SELEX, 3 experiments	best	0.991	0.986	0.968	0.95	0.912	0.892

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.93	0.735	0.892	0.638

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.1.SM.B.pcm
PWM	CUX2.H12RSNP.1.SM.B.pwm
PFM	CUX2.H12RSNP.1.SM.B.pfm
Alignment	CUX2.H12RSNP.1.SM.B.words.tsv
Threshold to P-value map	CUX2.H12RSNP.1.SM.B.thr
Motif in other formats
JASPAR format	CUX2.H12RSNP.1.SM.B_jaspar_format.txt
MEME format	CUX2.H12RSNP.1.SM.B_meme_format.meme
Transfac format	CUX2.H12RSNP.1.SM.B_transfac_format.txt
Homer format	CUX2.H12RSNP.1.SM.B_homer_format_0.001.txt CUX2.H12RSNP.1.SM.B_homer_format_0.0005.txt CUX2.H12RSNP.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2128.25	1248.25	1682.25	1976.25
02	846.0	644.0	1824.0	3721.0
03	360.0	233.0	608.0	5834.0
04	7035.0	0.0	0.0	0.0
05	0.0	0.0	0.0	7035.0
06	0.0	6436.0	0.0	599.0
07	0.0	0.0	7035.0	0.0
08	7035.0	0.0	0.0	0.0
09	0.0	0.0	0.0	7035.0
10	266.0	2160.0	43.0	4566.0
11	5536.0	716.0	225.0	558.0
12	1046.5	1961.5	1870.5	2156.5
13	1132.25	2304.25	1518.25	2080.25

PFM

	A	C	G	T
01	0.303	0.177	0.239	0.281
02	0.12	0.092	0.259	0.529
03	0.051	0.033	0.086	0.829
04	1.0	0.0	0.0	0.0
05	0.0	0.0	0.0	1.0
06	0.0	0.915	0.0	0.085
07	0.0	0.0	1.0	0.0
08	1.0	0.0	0.0	0.0
09	0.0	0.0	0.0	1.0
10	0.038	0.307	0.006	0.649
11	0.787	0.102	0.032	0.079
12	0.149	0.279	0.266	0.307
13	0.161	0.328	0.216	0.296

PWM

	A	C	G	T
01	0.19	-0.342	-0.044	0.116
02	-0.73	-1.002	0.036	0.749
03	-1.581	-2.013	-1.06	1.198
04	1.385	-6.679	-6.679	-6.679
05	-6.679	-6.679	-6.679	1.385
06	-6.679	1.296	-6.679	-1.075
07	-6.679	-6.679	1.385	-6.679
08	1.385	-6.679	-6.679	-6.679
09	-6.679	-6.679	-6.679	1.385
10	-1.882	0.205	-3.662	0.953
11	1.146	-0.897	-2.048	-1.145
12	-0.518	0.109	0.062	0.204
13	-0.44	0.27	-0.147	0.168

Standard thresholds

P-value	Threshold
0.001	0.30066
0.0005	1.97964
0.0001	6.429685