CUX1.H12RSNP.0.PM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CUX1.H12RSNP.0.PM.A
Gene (human)	CUX1 (GeneCards)
Gene synonyms (human)	CUTL1
Gene (mouse)	Cux1
Gene synonyms (mouse)	Cutl1, Cux, Kiaa4047
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	11
Consensus	dWKATTGATYd
GC content	21.22%
Information content (bits; total / per base)	12.978 / 1.18
Data sources	ChIP-Seq + Methyl-HT-SELEX
Aligned words	1000

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)	0.857	0.929	0.755	0.886	0.776	0.897	2.563	3.964	185.973	345.201

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.984	0.971	0.979	0.964	0.946	0.92
Overall, 4 experiments	best	0.991	0.984	0.989	0.98	0.985	0.974
Methyl HT-SELEX, 1 experiments	median	0.988	0.976	0.986	0.974	0.978	0.965
Methyl HT-SELEX, 1 experiments	best	0.988	0.976	0.986	0.974	0.978	0.965
Non-Methyl HT-SELEX, 3 experiments	median	0.98	0.965	0.972	0.954	0.915	0.875
Non-Methyl HT-SELEX, 3 experiments	best	0.991	0.984	0.989	0.98	0.985	0.974

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.941	0.841	0.895	0.571
batch 2	0.929	0.79	0.895	0.602

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.H12RSNP.0.PM.A.pcm
PWM	CUX1.H12RSNP.0.PM.A.pwm
PFM	CUX1.H12RSNP.0.PM.A.pfm
Alignment	CUX1.H12RSNP.0.PM.A.words.tsv
Threshold to P-value map	CUX1.H12RSNP.0.PM.A.thr
Motif in other formats
JASPAR format	CUX1.H12RSNP.0.PM.A_jaspar_format.txt
MEME format	CUX1.H12RSNP.0.PM.A_meme_format.meme
Transfac format	CUX1.H12RSNP.0.PM.A_transfac_format.txt
Homer format	CUX1.H12RSNP.0.PM.A_homer_format_0.001.txt CUX1.H12RSNP.0.PM.A_homer_format_0.0005.txt CUX1.H12RSNP.0.PM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	331.0	59.0	115.0	495.0
02	145.0	107.0	105.0	643.0
03	81.0	84.0	166.0	669.0
04	985.0	3.0	10.0	2.0
05	13.0	6.0	4.0	977.0
06	11.0	75.0	10.0	904.0
07	4.0	7.0	988.0	1.0
08	985.0	3.0	9.0	3.0
09	18.0	13.0	6.0	963.0
10	69.0	250.0	28.0	653.0
11	473.0	84.0	202.0	241.0

PFM

	A	C	G	T
01	0.331	0.059	0.115	0.495
02	0.145	0.107	0.105	0.643
03	0.081	0.084	0.166	0.669
04	0.985	0.003	0.01	0.002
05	0.013	0.006	0.004	0.977
06	0.011	0.075	0.01	0.904
07	0.004	0.007	0.988	0.001
08	0.985	0.003	0.009	0.003
09	0.018	0.013	0.006	0.963
10	0.069	0.25	0.028	0.653
11	0.473	0.084	0.202	0.241

PWM

	A	C	G	T
01	0.279	-1.422	-0.769	0.68
02	-0.54	-0.84	-0.858	0.94
03	-1.113	-1.077	-0.406	0.98
04	1.366	-3.975	-3.066	-4.213
05	-2.839	-3.484	-3.783	1.358
06	-2.985	-1.188	-3.066	1.28
07	-3.783	-3.362	1.369	-4.525
08	1.366	-3.975	-3.156	-3.975
09	-2.546	-2.839	-3.484	1.344
10	-1.27	0.0	-2.136	0.956
11	0.634	-1.077	-0.212	-0.036

Standard thresholds

P-value	Threshold
0.001	3.606305
0.0005	4.719115
0.0001	7.11587