CUX2.H12INVIVO.0.P.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CUX2.H12INVIVO.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	10
Consensus	bbATTGATYd
GC content	26.09%
Information content (bits; total / per base)	11.457 / 1.146
Data sources	ChIP-Seq
Aligned words	962

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)	0.853	0.891	0.793	0.838	0.827	0.861	3.014	3.245	213.745	256.027

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.942	0.902	0.854	0.829	0.679	0.703
Overall, 4 experiments	best	0.952	0.915	0.949	0.91	0.903	0.868
Methyl HT-SELEX, 1 experiments	median	0.942	0.895	0.858	0.83	0.685	0.706
Methyl HT-SELEX, 1 experiments	best	0.942	0.895	0.858	0.83	0.685	0.706
Non-Methyl HT-SELEX, 3 experiments	median	0.943	0.909	0.849	0.828	0.674	0.701
Non-Methyl HT-SELEX, 3 experiments	best	0.952	0.915	0.949	0.91	0.903	0.868

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.888	0.627	0.848	0.569

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.H12INVIVO.0.P.C.pcm
PWM	CUX2.H12INVIVO.0.P.C.pwm
PFM	CUX2.H12INVIVO.0.P.C.pfm
Alignment	CUX2.H12INVIVO.0.P.C.words.tsv
Threshold to P-value map	CUX2.H12INVIVO.0.P.C.thr
Motif in other formats
JASPAR format	CUX2.H12INVIVO.0.P.C_jaspar_format.txt
MEME format	CUX2.H12INVIVO.0.P.C_meme_format.meme
Transfac format	CUX2.H12INVIVO.0.P.C_transfac_format.txt
Homer format	CUX2.H12INVIVO.0.P.C_homer_format_0.001.txt CUX2.H12INVIVO.0.P.C_homer_format_0.0005.txt CUX2.H12INVIVO.0.P.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	124.0	177.0	142.0	519.0
02	69.0	205.0	209.0	479.0
03	927.0	13.0	10.0	12.0
04	14.0	6.0	50.0	892.0
05	12.0	62.0	20.0	868.0
06	4.0	1.0	948.0	9.0
07	934.0	9.0	8.0	11.0
08	26.0	45.0	8.0	883.0
09	21.0	237.0	17.0	687.0
10	201.0	92.0	251.0	418.0

PFM

	A	C	G	T
01	0.129	0.184	0.148	0.54
02	0.072	0.213	0.217	0.498
03	0.964	0.014	0.01	0.012
04	0.015	0.006	0.052	0.927
05	0.012	0.064	0.021	0.902
06	0.004	0.001	0.985	0.009
07	0.971	0.009	0.008	0.011
08	0.027	0.047	0.008	0.918
09	0.022	0.246	0.018	0.714
10	0.209	0.096	0.261	0.435

PWM

	A	C	G	T
01	-0.656	-0.304	-0.522	0.765
02	-1.231	-0.158	-0.139	0.685
03	1.344	-2.801	-3.029	-2.871
04	-2.735	-3.446	-1.544	1.306
05	-2.871	-1.335	-2.412	1.278
06	-3.746	-4.49	1.366	-3.118
07	1.351	-3.118	-3.216	-2.947
08	-2.168	-1.646	-3.216	1.295
09	-2.367	-0.015	-2.56	1.045
10	-0.178	-0.95	0.042	0.55

Standard thresholds

P-value	Threshold
0.001	4.34681
0.0005	5.26251
0.0001	7.30093