CXXC4.H13INVITRO.0.PSGIB.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CXXC4.H13INVITRO.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	9
Consensus	nTACGTbvn
GC content	51.57%
Information content (bits; total / per base)	8.403 / 0.934
Data sources	ChIP-Seq + HT-SELEX + Genomic HT-SELEX + SMiLe-Seq + PBM
Aligned words	588
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)	0.694	0.7	0.518	0.524	0.472	0.476	11.095	14.721

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
overall, 5 experiments	median	0.866	0.819	0.811	0.76	0.743	0.703
overall, 5 experiments	best	0.953	0.932	0.932	0.899	0.898	0.86
Lysate, 2 experiments	median	0.95	0.928	0.929	0.894	0.893	0.853
Lysate, 2 experiments	best	0.953	0.932	0.932	0.899	0.898	0.86
IVT, 2 experiments	median	0.674	0.619	0.648	0.599	0.613	0.579
IVT, 2 experiments	best	0.726	0.662	0.689	0.633	0.645	0.605
GFPIVT, 1 experiments	median	0.866	0.819	0.811	0.76	0.743	0.703
GFPIVT, 1 experiments	best	0.866	0.819	0.811	0.76	0.743	0.703

Genomic HT-SELEX benchmarking		Centrality	pseudo-auROC	auROC	auPR
overall, 3 experiments	median	4.481	0.371	0.907	0.835
overall, 3 experiments	best	157.0	0.548	0.945	0.903
Lysate, 2 experiments	median	155.101	0.544	0.922	0.835
Lysate, 2 experiments	best	157.0	0.548	0.922	0.837
GFPIVT, 1 experiments	median	1.824	0.365	0.871	0.837
GFPIVT, 1 experiments	best	7.137	0.373	0.945	0.903

SMiLE-Seq benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 1 experiments	median	0.708	0.655	0.659	0.617	0.607	0.584
Overall, 1 experiments	best	0.708	0.655	0.659	0.617	0.607	0.584

PBM benchmarking		auROC, QNZS	auPR, QNZS	auROC, SD	auPR, SD
Overall, 8 experiments	median	0.927	0.035	0.927	0.061
Overall, 8 experiments	best	0.939	0.041	0.939	0.077

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.H13INVITRO.0.PSGIB.A.pcm
PWM	CXXC4.H13INVITRO.0.PSGIB.A.pwm
PFM	CXXC4.H13INVITRO.0.PSGIB.A.pfm
Threshold to P-value map	CXXC4.H13INVITRO.0.PSGIB.A.thr
Motif in other formats
JASPAR format	CXXC4.H13INVITRO.0.PSGIB.A_jaspar_format.txt
MEME format	CXXC4.H13INVITRO.0.PSGIB.A_meme_format.meme
Transfac format	CXXC4.H13INVITRO.0.PSGIB.A_transfac_format.txt
Homer format	CXXC4.H13INVITRO.0.PSGIB.A_homer_format_0.001.txt CXXC4.H13INVITRO.0.PSGIB.A_homer_format_0.0005.txt CXXC4.H13INVITRO.0.PSGIB.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	129.0	86.0	187.0	186.0
02	34.0	110.0	0.0	444.0
03	309.0	0.0	279.0	0.0
04	0.0	588.0	0.0	0.0
05	0.0	0.0	588.0	0.0
06	0.0	0.0	0.0	588.0
07	67.0	182.0	181.0	158.0
08	285.0	103.0	145.0	55.0
09	148.0	163.0	117.0	160.0

PFM

	A	C	G	T
01	0.219	0.146	0.318	0.316
02	0.058	0.187	0.0	0.755
03	0.526	0.0	0.474	0.0
04	0.0	1.0	0.0	0.0
05	0.0	0.0	1.0	0.0
06	0.0	0.0	0.0	1.0
07	0.114	0.31	0.308	0.269
08	0.485	0.175	0.247	0.094
09	0.252	0.277	0.199	0.272

PWM

	A	C	G	T
01	-0.129	-0.529	0.238	0.233
02	-1.429	-0.286	-4.535	1.098
03	0.737	-4.535	0.636	-4.535
04	-4.535	1.378	-4.535	-4.535
05	-4.535	-4.535	1.378	-4.535
06	-4.535	-4.535	-4.535	1.378
07	-0.773	0.212	0.206	0.071
08	0.657	-0.351	-0.014	-0.965
09	0.007	0.102	-0.226	0.084

Standard thresholds

P-value	Threshold
0.001	5.674605
0.0005	6.16906
0.0001	6.974625