CUX2.H12INVIVO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CUX2.H12INVIVO.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	11
Consensus	nYATCGATYMn
GC content	33.09%
Information content (bits; total / per base)	12.675 / 1.152
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	6676

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)	0.865	0.889	0.82	0.842	0.795	0.829	2.638	2.895	215.377	263.125

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.982	0.969	0.88	0.881	0.686	0.73
Overall, 4 experiments	best	0.992	0.987	0.971	0.954	0.922	0.903
Methyl HT-SELEX, 1 experiments	median	0.983	0.972	0.878	0.874	0.69	0.729
Methyl HT-SELEX, 1 experiments	best	0.983	0.972	0.878	0.874	0.69	0.729
Non-Methyl HT-SELEX, 3 experiments	median	0.981	0.966	0.882	0.888	0.682	0.731
Non-Methyl HT-SELEX, 3 experiments	best	0.992	0.987	0.971	0.954	0.922	0.903

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.92	0.668	0.878	0.625

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.1.SM.B.pcm
PWM	CUX2.H12INVIVO.1.SM.B.pwm
PFM	CUX2.H12INVIVO.1.SM.B.pfm
Alignment	CUX2.H12INVIVO.1.SM.B.words.tsv
Threshold to P-value map	CUX2.H12INVIVO.1.SM.B.thr
Motif in other formats
JASPAR format	CUX2.H12INVIVO.1.SM.B_jaspar_format.txt
MEME format	CUX2.H12INVIVO.1.SM.B_meme_format.meme
Transfac format	CUX2.H12INVIVO.1.SM.B_transfac_format.txt
Homer format	CUX2.H12INVIVO.1.SM.B_homer_format_0.001.txt CUX2.H12INVIVO.1.SM.B_homer_format_0.0005.txt CUX2.H12INVIVO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1538.25	1168.25	1533.25	2436.25
02	522.25	876.25	861.25	4416.25
03	6148.0	48.0	50.0	430.0
04	0.0	0.0	1.0	6675.0
05	0.0	5642.0	0.0	1034.0
06	0.0	0.0	6676.0	0.0
07	6676.0	0.0	0.0	0.0
08	0.0	14.0	14.0	6648.0
09	569.0	2460.0	75.0	3572.0
10	4470.25	1027.25	490.25	688.25
11	1373.5	1747.5	1617.5	1937.5

PFM

	A	C	G	T
01	0.23	0.175	0.23	0.365
02	0.078	0.131	0.129	0.662
03	0.921	0.007	0.007	0.064
04	0.0	0.0	0.0	1.0
05	0.0	0.845	0.0	0.155
06	0.0	0.0	1.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.002	0.002	0.996
09	0.085	0.368	0.011	0.535
10	0.67	0.154	0.073	0.103
11	0.206	0.262	0.242	0.29

PWM

	A	C	G	T
01	-0.081	-0.356	-0.085	0.378
02	-1.159	-0.643	-0.66	0.972
03	1.303	-3.505	-3.466	-1.352
04	-6.632	-6.632	-6.258	1.385
05	-6.632	1.217	-6.632	-0.478
06	-6.632	-6.632	1.385	-6.632
07	1.385	-6.632	-6.632	-6.632
08	-6.632	-4.636	-4.636	1.381
09	-1.074	0.388	-3.075	0.76
10	0.984	-0.485	-1.222	-0.884
11	-0.195	0.046	-0.031	0.149

Standard thresholds

P-value	Threshold
0.001	2.705765
0.0005	4.51734
0.0001	7.387755