CUX2.H12INVITRO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CUX2.H12INVITRO.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	nbWTCGAThhn
GC content	35.57%
Information content (bits; total / per base)	10.51 / 0.955
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9764

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)	0.87	0.891	0.826	0.847	0.787	0.822	2.559	2.813	207.022	255.585

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.984	0.971	0.884	0.885	0.695	0.735
Overall, 4 experiments	best	0.992	0.989	0.972	0.955	0.931	0.91
Methyl HT-SELEX, 1 experiments	median	0.985	0.975	0.885	0.88	0.701	0.736
Methyl HT-SELEX, 1 experiments	best	0.985	0.975	0.885	0.88	0.701	0.736
Non-Methyl HT-SELEX, 3 experiments	median	0.982	0.968	0.882	0.889	0.688	0.734
Non-Methyl HT-SELEX, 3 experiments	best	0.992	0.989	0.972	0.955	0.931	0.91

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.918	0.615	0.86	0.613

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.H12INVITRO.1.SM.B.pcm
PWM	CUX2.H12INVITRO.1.SM.B.pwm
PFM	CUX2.H12INVITRO.1.SM.B.pfm
Alignment	CUX2.H12INVITRO.1.SM.B.words.tsv
Threshold to P-value map	CUX2.H12INVITRO.1.SM.B.thr
Motif in other formats
JASPAR format	CUX2.H12INVITRO.1.SM.B_jaspar_format.txt
MEME format	CUX2.H12INVITRO.1.SM.B_meme_format.meme
Transfac format	CUX2.H12INVITRO.1.SM.B_transfac_format.txt
Homer format	CUX2.H12INVITRO.1.SM.B_homer_format_0.001.txt CUX2.H12INVITRO.1.SM.B_homer_format_0.0005.txt CUX2.H12INVITRO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2264.75	1981.75	2237.75	3279.75
02	1038.0	1691.0	1630.0	5405.0
03	7316.0	476.0	476.0	1496.0
04	82.0	96.0	174.0	9412.0
05	1.0	7644.0	26.0	2093.0
06	0.0	5.0	9759.0	0.0
07	9609.0	95.0	45.0	15.0
08	16.0	140.0	153.0	9455.0
09	1439.0	3435.0	304.0	4586.0
10	5633.0	1749.0	1159.0	1223.0
11	2091.0	2540.0	2385.0	2748.0

PFM

	A	C	G	T
01	0.232	0.203	0.229	0.336
02	0.106	0.173	0.167	0.554
03	0.749	0.049	0.049	0.153
04	0.008	0.01	0.018	0.964
05	0.0	0.783	0.003	0.214
06	0.0	0.001	0.999	0.0
07	0.984	0.01	0.005	0.002
08	0.002	0.014	0.016	0.968
09	0.147	0.352	0.031	0.47
10	0.577	0.179	0.119	0.125
11	0.214	0.26	0.244	0.281

PWM

	A	C	G	T
01	-0.075	-0.208	-0.087	0.295
02	-0.854	-0.367	-0.403	0.794
03	1.097	-1.631	-1.631	-0.489
04	-3.367	-3.213	-2.629	1.349
05	-6.608	1.141	-4.458	-0.154
06	-6.97	-5.814	1.385	-6.97
07	1.37	-3.223	-3.945	-4.951
08	-4.894	-2.843	-2.756	1.353
09	-0.528	0.341	-2.077	0.63
10	0.836	-0.333	-0.744	-0.69
11	-0.155	0.04	-0.023	0.118

Standard thresholds

P-value	Threshold
0.001	4.54122
0.0005	5.72485
0.0001	7.507295