CXXC4.H14INVIVO.0.PSGIB.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CXXC4.H14INVIVO.0.PSGIB.A
Gene (human)	CXXC4 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Cxxc4
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	21
Consensus	RvSdvRGvGGCGGvGvbbSvR
GC content	79.46%
Information content (bits; total / per base)	15.547 / 0.74
Data sources	ChIP-Seq + HT-SELEX + Genomic HT-SELEX + SMiLe-Seq + PBM
Aligned words	499
Previous names

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	Centrality, median	Centrality, best
Overall	2 (2)	0.776	0.785	0.551	0.563	0.673	0.703	18.594	22.301

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
overall, 5 experiments	median	0.507	0.503	0.511	0.504	0.512	0.506
overall, 5 experiments	best	0.54	0.522	0.532	0.518	0.524	0.515
Lysate, 2 experiments	median	0.508	0.503	0.512	0.505	0.513	0.506
Lysate, 2 experiments	best	0.509	0.503	0.512	0.505	0.514	0.506
IVT, 2 experiments	median	0.484	0.49	0.492	0.494	0.497	0.497
IVT, 2 experiments	best	0.497	0.495	0.504	0.499	0.507	0.502
GFPIVT, 1 experiments	median	0.54	0.522	0.532	0.518	0.524	0.515
GFPIVT, 1 experiments	best	0.54	0.522	0.532	0.518	0.524	0.515

Genomic HT-SELEX benchmarking		Centrality	pseudo-auROC	auROC	auPR
overall, 3 experiments	median	0.0	0.432	0.479	0.326
overall, 3 experiments	best	0.0	0.566	0.521	0.357
Lysate, 2 experiments	median	0.0	0.561	0.52	0.355
Lysate, 2 experiments	best	0.0	0.566	0.521	0.357
GFPIVT, 1 experiments	median	0.0	0.412	0.45	0.307
GFPIVT, 1 experiments	best	0.0	0.45	0.496	0.339

SMiLE-Seq benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 1 experiments	median	0.458	0.486	0.478	0.489	0.49	0.493
Overall, 1 experiments	best	0.458	0.486	0.478	0.489	0.49	0.493

PBM benchmarking		auROC, QNZS	auPR, QNZS	auROC, SD	auPR, SD
Overall, 8 experiments	median	0.607	0.002	0.551	0.005
Overall, 8 experiments	best	0.649	0.002	0.601	0.01

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	CXXC zinc finger factors {2.6} (TFClass)
TF family	CpG-binding {2.6.1} (TFClass)
TF subfamily	{2.6.1.0} (TFClass)
TFClass ID	TFClass: 2.6.1.0.255
HGNC
MGI
EntrezGene (human)
EntrezGene (mouse)
UniProt ID (human)	CXXC4_HUMAN
UniProt ID (mouse)	CXXC4_MOUSE
UniProt AC (human)	Q9H2H0 (TFClass)
UniProt AC (mouse)	Q6NXI8 (TFClass)
GRECO-DB-TF	no

ChIP-Seq	2 human, 0 mouse
HT-SELEX	5 overall: 2 Lysate, 2 IVT, 1 GFPIVT
Genomic HT-SELEX	3 overall: 2 Lysate, 0 IVT, 1 GFPIVT
SMiLE-Seq	1
PBM	8

PCM	CXXC4.H14INVIVO.0.PSGIB.A.pcm
PWM	CXXC4.H14INVIVO.0.PSGIB.A.pwm
PFM	CXXC4.H14INVIVO.0.PSGIB.A.pfm
Threshold to P-value map	CXXC4.H14INVIVO.0.PSGIB.A.thr
Motif in other formats
JASPAR format	CXXC4.H14INVIVO.0.PSGIB.A_jaspar_format.txt
MEME format	CXXC4.H14INVIVO.0.PSGIB.A_meme_format.meme
Transfac format	CXXC4.H14INVIVO.0.PSGIB.A_transfac_format.txt
Homer format	CXXC4.H14INVIVO.0.PSGIB.A_homer_format_0.001.txt CXXC4.H14INVIVO.0.PSGIB.A_homer_format_0.0005.txt CXXC4.H14INVIVO.0.PSGIB.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	68.0	33.0	375.0	23.0
02	149.0	176.0	117.0	57.0
03	36.0	47.0	393.0	23.0
04	99.0	63.0	259.0	78.0
05	119.0	172.0	158.0	50.0
06	142.0	27.0	306.0	24.0
07	72.0	13.0	401.0	13.0
08	114.0	175.0	194.0	16.0
09	27.0	32.0	403.0	37.0
10	19.0	4.0	468.0	8.0
11	36.0	458.0	2.0	3.0
12	11.0	14.0	458.0	16.0
13	14.0	10.0	447.0	28.0
14	101.0	167.0	194.0	37.0
15	27.0	13.0	449.0	10.0
16	81.0	234.0	149.0	35.0
17	21.0	266.0	128.0	84.0
18	33.0	68.0	248.0	150.0
19	47.0	54.0	376.0	22.0
20	89.0	244.0	141.0	25.0
21	87.0	46.0	345.0	21.0

PFM

	A	C	G	T
01	0.136	0.066	0.752	0.046
02	0.299	0.353	0.234	0.114
03	0.072	0.094	0.788	0.046
04	0.198	0.126	0.519	0.156
05	0.238	0.345	0.317	0.1
06	0.285	0.054	0.613	0.048
07	0.144	0.026	0.804	0.026
08	0.228	0.351	0.389	0.032
09	0.054	0.064	0.808	0.074
10	0.038	0.008	0.938	0.016
11	0.072	0.918	0.004	0.006
12	0.022	0.028	0.918	0.032
13	0.028	0.02	0.896	0.056
14	0.202	0.335	0.389	0.074
15	0.054	0.026	0.9	0.02
16	0.162	0.469	0.299	0.07
17	0.042	0.533	0.257	0.168
18	0.066	0.136	0.497	0.301
19	0.094	0.108	0.754	0.044
20	0.178	0.489	0.283	0.05
21	0.174	0.092	0.691	0.042

PWM

	A	C	G	T
01	-0.597	-1.296	1.092	-1.638
02	0.176	0.341	-0.063	-0.769
03	-1.213	-0.956	1.139	-1.638
04	-0.228	-0.671	0.724	-0.462
05	-0.047	0.318	0.234	-0.896
06	0.128	-1.487	0.89	-1.598
07	-0.541	-2.161	1.159	-2.161
08	-0.089	0.335	0.437	-1.973
09	-1.487	-1.326	1.164	-1.187
10	-1.816	-3.124	1.313	-2.582
11	-1.213	1.292	-3.571	-3.323
12	-2.309	-2.094	1.292	-1.973
13	-2.094	-2.392	1.267	-1.452
14	-0.208	0.289	0.437	-1.187
15	-1.487	-2.161	1.272	-2.392
16	-0.425	0.623	0.176	-1.24
17	-1.723	0.751	0.025	-0.39
18	-1.296	-0.597	0.681	0.182
19	-0.956	-0.821	1.095	-1.679
20	-0.333	0.665	0.121	-1.56
21	-0.355	-0.977	1.009	-1.723

Standard thresholds

P-value	Threshold
0.001	3.24036
0.0005	4.29156
0.0001	6.52251