CUX1.H12INVIVO.0.PM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CUX1.H12INVIVO.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	13
Consensus	bbATTGAThhnbn
GC content	31.49%
Information content (bits; total / per base)	11.277 / 0.867
Data sources	ChIP-Seq + Methyl-HT-SELEX
Aligned words	733

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)	0.882	0.939	0.799	0.902	0.799	0.903	2.705	3.863	231.887	364.06

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.989	0.98	0.984	0.973	0.956	0.934
Overall, 4 experiments	best	0.995	0.99	0.993	0.987	0.99	0.983
Methyl HT-SELEX, 1 experiments	median	0.992	0.985	0.989	0.981	0.984	0.974
Methyl HT-SELEX, 1 experiments	best	0.992	0.985	0.989	0.981	0.984	0.974
Non-Methyl HT-SELEX, 3 experiments	median	0.986	0.975	0.979	0.965	0.927	0.893
Non-Methyl HT-SELEX, 3 experiments	best	0.995	0.99	0.993	0.987	0.99	0.983

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.952	0.82	0.913	0.606
batch 2	0.919	0.778	0.882	0.62

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.0.PM.A.pcm
PWM	CUX1.H12INVIVO.0.PM.A.pwm
PFM	CUX1.H12INVIVO.0.PM.A.pfm
Alignment	CUX1.H12INVIVO.0.PM.A.words.tsv
Threshold to P-value map	CUX1.H12INVIVO.0.PM.A.thr
Motif in other formats
JASPAR format	CUX1.H12INVIVO.0.PM.A_jaspar_format.txt
MEME format	CUX1.H12INVIVO.0.PM.A_meme_format.meme
Transfac format	CUX1.H12INVIVO.0.PM.A_transfac_format.txt
Homer format	CUX1.H12INVIVO.0.PM.A_homer_format_0.001.txt CUX1.H12INVIVO.0.PM.A_homer_format_0.0005.txt CUX1.H12INVIVO.0.PM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	116.0	147.0	153.0	317.0
02	69.0	107.0	122.0	435.0
03	709.0	2.0	7.0	15.0
04	3.0	4.0	2.0	724.0
05	11.0	99.0	10.0	613.0
06	1.0	2.0	723.0	7.0
07	713.0	5.0	6.0	9.0
08	24.0	31.0	7.0	671.0
09	104.0	317.0	24.0	288.0
10	345.0	128.0	81.0	179.0
11	153.0	158.0	202.0	220.0
12	106.0	153.0	152.0	322.0
13	136.0	139.0	220.0	238.0

PFM

	A	C	G	T
01	0.158	0.201	0.209	0.432
02	0.094	0.146	0.166	0.593
03	0.967	0.003	0.01	0.02
04	0.004	0.005	0.003	0.988
05	0.015	0.135	0.014	0.836
06	0.001	0.003	0.986	0.01
07	0.973	0.007	0.008	0.012
08	0.033	0.042	0.01	0.915
09	0.142	0.432	0.033	0.393
10	0.471	0.175	0.111	0.244
11	0.209	0.216	0.276	0.3
12	0.145	0.209	0.207	0.439
13	0.186	0.19	0.3	0.325

PWM

	A	C	G	T
01	-0.452	-0.218	-0.179	0.544
02	-0.962	-0.532	-0.402	0.859
03	1.346	-3.925	-3.062	-2.407
04	-3.683	-3.488	-3.925	1.367
05	-2.682	-0.608	-2.765	1.201
06	-4.246	-3.925	1.366	-3.062
07	1.352	-3.325	-3.185	-2.854
08	-1.975	-1.734	-3.062	1.291
09	-0.56	0.544	-1.975	0.449
10	0.629	-0.355	-0.805	-0.023
11	-0.179	-0.147	0.097	0.181
12	-0.541	-0.179	-0.185	0.56
13	-0.295	-0.274	0.181	0.259

Standard thresholds

P-value	Threshold
0.001	4.30041
0.0005	5.26506
0.0001	7.51982