CUX1.H12INVIVO.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CUX1.H12INVIVO.1.S.B
Gene (human)	CUX1 (GeneCards)
Gene synonyms (human)	CUTL1
Gene (mouse)	Cux1
Gene synonyms (mouse)	Cutl1, Cux, Kiaa4047
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	14
Consensus	nbKATCGATYRnnn
GC content	38.2%
Information content (bits; total / per base)	13.61 / 0.972
Data sources	HT-SELEX
Aligned words	8038

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)	0.856	0.928	0.799	0.897	0.784	0.892	2.503	3.43	217.298	345.602

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.991	0.983	0.987	0.978	0.962	0.944
Overall, 4 experiments	best	0.998	0.997	0.998	0.996	0.996	0.993
Methyl HT-SELEX, 1 experiments	median	0.989	0.978	0.986	0.975	0.983	0.97
Methyl HT-SELEX, 1 experiments	best	0.989	0.978	0.986	0.975	0.983	0.97
Non-Methyl HT-SELEX, 3 experiments	median	0.993	0.988	0.988	0.98	0.942	0.919
Non-Methyl HT-SELEX, 3 experiments	best	0.998	0.997	0.998	0.996	0.996	0.993

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.947	0.848	0.934	0.646
batch 2	0.906	0.785	0.88	0.626

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.H12INVIVO.1.S.B.pcm
PWM	CUX1.H12INVIVO.1.S.B.pwm
PFM	CUX1.H12INVIVO.1.S.B.pfm
Alignment	CUX1.H12INVIVO.1.S.B.words.tsv
Threshold to P-value map	CUX1.H12INVIVO.1.S.B.thr
Motif in other formats
JASPAR format	CUX1.H12INVIVO.1.S.B_jaspar_format.txt
MEME format	CUX1.H12INVIVO.1.S.B_meme_format.meme
Transfac format	CUX1.H12INVIVO.1.S.B_transfac_format.txt
Homer format	CUX1.H12INVIVO.1.S.B_homer_format_0.001.txt CUX1.H12INVIVO.1.S.B_homer_format_0.0005.txt CUX1.H12INVIVO.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2196.25	1758.25	2157.25	1926.25
02	1022.75	1809.75	2395.75	2809.75
03	784.0	616.0	1512.0	5126.0
04	8022.0	0.0	0.0	16.0
05	0.0	0.0	0.0	8038.0
06	0.0	6744.0	0.0	1294.0
07	0.0	0.0	8038.0	0.0
08	8038.0	0.0	0.0	0.0
09	0.0	0.0	1.0	8037.0
10	605.0	3179.0	2.0	4252.0
11	6094.0	649.0	861.0	434.0
12	1798.0	2296.0	2672.0	1272.0
13	1105.75	2638.75	1982.75	2310.75
14	2004.25	1789.25	1890.25	2354.25

PFM

	A	C	G	T
01	0.273	0.219	0.268	0.24
02	0.127	0.225	0.298	0.35
03	0.098	0.077	0.188	0.638
04	0.998	0.0	0.0	0.002
05	0.0	0.0	0.0	1.0
06	0.0	0.839	0.0	0.161
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	0.075	0.395	0.0	0.529
11	0.758	0.081	0.107	0.054
12	0.224	0.286	0.332	0.158
13	0.138	0.328	0.247	0.287
14	0.249	0.223	0.235	0.293

PWM

	A	C	G	T
01	0.089	-0.133	0.071	-0.042
02	-0.674	-0.105	0.176	0.335
03	-0.939	-1.18	-0.284	0.936
04	1.383	-6.797	-6.797	-4.703
05	-6.797	-6.797	-6.797	1.385
06	-6.797	1.21	-6.797	-0.44
07	-6.797	-6.797	1.385	-6.797
08	1.385	-6.797	-6.797	-6.797
09	-6.797	-6.797	-6.429	1.385
10	-1.198	0.458	-6.16	0.749
11	1.109	-1.128	-0.846	-1.529
12	-0.111	0.133	0.285	-0.457
13	-0.596	0.272	-0.013	0.14
14	-0.003	-0.116	-0.061	0.158

Standard thresholds

P-value	Threshold
0.001	0.78751
0.0005	2.30116
0.0001	7.284865