CUX1.H12INVITRO.0.PM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CUX1.H12INVITRO.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	10
Consensus	nbATTGAThh
GC content	27.2%
Information content (bits; total / per base)	10.548 / 1.055
Data sources	ChIP-Seq + Methyl-HT-SELEX
Aligned words	1002

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)	0.891	0.944	0.802	0.905	0.793	0.899	2.57	3.615	220.773	353.194

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.989	0.98	0.984	0.973	0.958	0.935
Overall, 4 experiments	best	0.996	0.993	0.994	0.989	0.99	0.984
Methyl HT-SELEX, 1 experiments	median	0.991	0.982	0.988	0.979	0.983	0.972
Methyl HT-SELEX, 1 experiments	best	0.991	0.982	0.988	0.979	0.983	0.972
Non-Methyl HT-SELEX, 3 experiments	median	0.988	0.979	0.98	0.967	0.932	0.897
Non-Methyl HT-SELEX, 3 experiments	best	0.996	0.993	0.994	0.989	0.99	0.984

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.944	0.817	0.904	0.58
batch 2	0.928	0.759	0.877	0.598

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.H12INVITRO.0.PM.A.pcm
PWM	CUX1.H12INVITRO.0.PM.A.pwm
PFM	CUX1.H12INVITRO.0.PM.A.pfm
Alignment	CUX1.H12INVITRO.0.PM.A.words.tsv
Threshold to P-value map	CUX1.H12INVITRO.0.PM.A.thr
Motif in other formats
JASPAR format	CUX1.H12INVITRO.0.PM.A_jaspar_format.txt
MEME format	CUX1.H12INVITRO.0.PM.A_meme_format.meme
Transfac format	CUX1.H12INVITRO.0.PM.A_transfac_format.txt
Homer format	CUX1.H12INVITRO.0.PM.A_homer_format_0.001.txt CUX1.H12INVITRO.0.PM.A_homer_format_0.0005.txt CUX1.H12INVITRO.0.PM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	178.0	176.0	178.0	470.0
02	89.0	201.0	163.0	549.0
03	986.0	3.0	6.0	7.0
04	8.0	34.0	5.0	955.0
05	43.0	144.0	18.0	797.0
06	1.0	2.0	995.0	4.0
07	968.0	10.0	19.0	5.0
08	36.0	49.0	22.0	895.0
09	176.0	356.0	61.0	409.0
10	494.0	167.0	116.0	225.0

PFM

	A	C	G	T
01	0.178	0.176	0.178	0.469
02	0.089	0.201	0.163	0.548
03	0.984	0.003	0.006	0.007
04	0.008	0.034	0.005	0.953
05	0.043	0.144	0.018	0.795
06	0.001	0.002	0.993	0.004
07	0.966	0.01	0.019	0.005
08	0.036	0.049	0.022	0.893
09	0.176	0.355	0.061	0.408
10	0.493	0.167	0.116	0.225

PWM

	A	C	G	T
01	-0.339	-0.35	-0.339	0.626
02	-1.022	-0.218	-0.426	0.781
03	1.365	-3.977	-3.486	-3.364
04	-3.255	-1.954	-3.624	1.333
05	-1.73	-0.549	-2.548	1.153
06	-4.527	-4.215	1.374	-3.785
07	1.347	-3.068	-2.499	-3.624
08	-1.9	-1.604	-2.364	1.268
09	-0.35	0.349	-1.392	0.488
10	0.676	-0.402	-0.762	-0.107

Standard thresholds

P-value	Threshold
0.001	4.568795
0.0005	5.500125
0.0001	7.562025