CUX1.H12INVIVO.2.P.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CUX1.H12INVIVO.2.P.C
Gene (human)	CUX1 (GeneCards)
Gene synonyms (human)	CUTL1
Gene (mouse)	Cux1
Gene synonyms (mouse)	Cutl1, Cux, Kiaa4047
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	C

Motif length	19
Consensus	WdATKGWKKndYWbWKKhY
GC content	41.56%
Information content (bits; total / per base)	12.208 / 0.643
Data sources	ChIP-Seq
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)	0.599	0.841	0.432	0.819	0.583	0.821	1.371	7.71	4.69	118.721

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.675	0.612	0.642	0.594	0.606	0.574
Overall, 4 experiments	best	0.734	0.659	0.706	0.64	0.666	0.616
Methyl HT-SELEX, 1 experiments	median	0.695	0.628	0.662	0.608	0.623	0.586
Methyl HT-SELEX, 1 experiments	best	0.695	0.628	0.662	0.608	0.623	0.586
Non-Methyl HT-SELEX, 3 experiments	median	0.654	0.597	0.622	0.579	0.588	0.561
Non-Methyl HT-SELEX, 3 experiments	best	0.734	0.659	0.706	0.64	0.666	0.616

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.547	0.136	0.418	0.243
batch 2	0.554	0.17	0.417	0.264

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.2.P.C.pcm
PWM	CUX1.H12INVIVO.2.P.C.pwm
PFM	CUX1.H12INVIVO.2.P.C.pfm
Alignment	CUX1.H12INVIVO.2.P.C.words.tsv
Threshold to P-value map	CUX1.H12INVIVO.2.P.C.thr
Motif in other formats
JASPAR format	CUX1.H12INVIVO.2.P.C_jaspar_format.txt
MEME format	CUX1.H12INVIVO.2.P.C_meme_format.meme
Transfac format	CUX1.H12INVIVO.2.P.C_transfac_format.txt
Homer format	CUX1.H12INVIVO.2.P.C_homer_format_0.001.txt CUX1.H12INVIVO.2.P.C_homer_format_0.0005.txt CUX1.H12INVIVO.2.P.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	716.0	17.0	45.0	222.0
02	169.0	116.0	575.0	140.0
03	864.0	58.0	47.0	31.0
04	49.0	11.0	96.0	844.0
05	56.0	25.0	653.0	266.0
06	49.0	80.0	837.0	34.0
07	784.0	78.0	44.0	94.0
08	31.0	37.0	573.0	359.0
09	108.0	81.0	125.0	686.0
10	144.0	278.0	232.0	346.0
11	446.0	75.0	374.0	105.0
12	35.0	562.0	120.0	283.0
13	198.0	51.0	34.0	717.0
14	153.0	413.0	254.0	180.0
15	289.0	58.0	67.0	586.0
16	85.0	30.0	464.0	421.0
17	73.0	55.0	762.0	110.0
18	196.0	182.0	72.0	550.0
19	61.0	213.0	102.0	624.0

PFM

	A	C	G	T
01	0.716	0.017	0.045	0.222
02	0.169	0.116	0.575	0.14
03	0.864	0.058	0.047	0.031
04	0.049	0.011	0.096	0.844
05	0.056	0.025	0.653	0.266
06	0.049	0.08	0.837	0.034
07	0.784	0.078	0.044	0.094
08	0.031	0.037	0.573	0.359
09	0.108	0.081	0.125	0.686
10	0.144	0.278	0.232	0.346
11	0.446	0.075	0.374	0.105
12	0.035	0.562	0.12	0.283
13	0.198	0.051	0.034	0.717
14	0.153	0.413	0.254	0.18
15	0.289	0.058	0.067	0.586
16	0.085	0.03	0.464	0.421
17	0.073	0.055	0.762	0.11
18	0.196	0.182	0.072	0.55
19	0.061	0.213	0.102	0.624

PWM

	A	C	G	T
01	1.048	-2.598	-1.684	-0.118
02	-0.388	-0.76	0.829	-0.574
03	1.235	-1.439	-1.642	-2.04
04	-1.602	-2.985	-0.946	1.212
05	-1.473	-2.243	0.956	0.062
06	-1.602	-1.125	1.204	-1.952
07	1.138	-1.15	-1.706	-0.967
08	-2.04	-1.872	0.826	0.36
09	-0.83	-1.113	-0.686	1.005
10	-0.547	0.105	-0.074	0.323
11	0.576	-1.188	0.401	-0.858
12	-1.925	0.806	-0.727	0.123
13	-0.231	-1.563	-1.952	1.049
14	-0.487	0.499	0.016	-0.326
15	0.144	-1.439	-1.298	0.848
16	-1.066	-2.071	0.615	0.518
17	-1.215	-1.49	1.11	-0.812
18	-0.241	-0.315	-1.228	0.785
19	-1.39	-0.159	-0.887	0.911

Standard thresholds

P-value	Threshold
0.001	4.22136
0.0005	5.10781
0.0001	6.98536