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CTCFBSDB specifications

Information


Unique identifier OMICS_00530
Name CTCFBSDB
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Version 2.0
Maintained Yes

Subtool


  • CTCFBS Prediction Tool

Maintainer


  • person_outline Yan Cui

Publications for CTCFBSDB

CTCFBSDB citations

 (14)
library_books

The long range interaction map of ribosomal DNA arrays

2018
PLoS Genet
PMCID: 5865718
PMID: 29570716
DOI: 10.1371/journal.pgen.1007258

[…] ed. Third, information on replication timing along the genome was downloaded from the Replication Domain Database (www.replicationdomain.org). Finally, CTCF binding coordinates were obtained from the CTCFBSDB database []. We extracted the coordinates for all the segments in each annotation and addressed its density of rDNA contacts. BEDTools was used to assess the number of mapped reads that overl […]

call_split

Association studies of WD repeat domain 3 and chitobiosyldiphosphodolichol beta mannosyltransferase genes with schizophrenia in a Japanese population

2018
PLoS One
PMCID: 5757935
PMID: 29309433
DOI: 10.1371/journal.pone.0190991
call_split See protocol

[…] Select algorithm to evaluate the selection of the SNPs []. Additionally, we added SNPs from the insulator regions (CTCF binding site) between the target and adjacent gene as an effective region using CTCFBSDB 2.0 (http://insulatordb.uthsc.edu/) [].SNP genotyping was performed by TaqMan SNP genotyping assays (Applied Biosystems, Foster City, CA, USA). We used an ABI PRISM 7900HT (Applied Biosystems […]

library_books

Identification and characterization of two functional variants in the human longevity gene FOXO3

2017
Nat Commun
PMCID: 5727304
PMID: 29234056
DOI: 10.1038/s41467-017-02183-y

[…] culating IGF-1 remains to be clarified.The CTCF supershift experiments indicated a slightly stronger binding of CTCF to the oligonucleotide containing the major allele C of rs12206094, confirming the CTCFBSDB 2.027 prediction. However, our functional experiments with the rs12206094 allele-specific constructs suggested that the binding strength of CTCF did not influence the luciferase promoter acti […]

library_books

Alternatively spliced MEFV transcript lacking exon 2 and its protein isoform pyrin 2d implies an epigenetic regulation of the gene in inflammatory cell culture models

2017
Genet Mol Biol
PMCID: 5596369
PMID: 28863210
DOI: 10.1590/1678-4685-GMB-2016-0234

[…] methylation (). Adversely, another protein, CTCF, was found to play a role in the recognition of a weak exon signal in the CD45 gene in the absence of DNA methylation (). Although our research on the CTCFBSDB database, a database for CTCF binding sites, has shown the absence of CTCF in the MEFV gene in HL-60 cells, the CTCF prediction tool on the same site predicts a binding site 35 bp from the ex […]

library_books

Expansion of epigenetic alterations in EFEMP1 promoter predicts malignant formation in pancreatobiliary intraductal papillary mucinous neoplasms

2016
PMCID: 4899496
PMID: 27095449
DOI: 10.1007/s00432-016-2164-x

[…] t various regions in previous studies (Kobayashi et al. ; Nomoto et al. ; Sadr-Nabavi et al. ; Wang et al. , ; Yang et al. ; Yue et al. ; Zhu et al. ). In this study, we searched CTCF biding sites by CTCFBSDB 2.0 (http://insulatordb.uthsc.edu/) in promoter region of the EFEMP1 gene and found a CTCF biding site ‘TGACATCTGTTGGG,’ called as the EMBL_M1 motifs (Schmidt et al. ). CTCF, also known as CC […]

library_books

Jointly characterizing epigenetic dynamics across multiple human cell types

2016
Nucleic Acids Res
PMCID: 5772166
PMID: 27095202
DOI: 10.1093/nar/gkw278

[…] contribute to the performance difference observed here.We next evaluated CTCF occupancy prediction using manually curated CTCF sites and experimentally validated CTCF sites from non-ENCODE studies in CTCFBSDB2.0 (). The CTCF-labeled states for IDEAS captured substantially more CTCF sites (57.7%) than for ChromHMM (21.2%) and Segway (25.0%), respectively, on the manually curated CTCF. Similarly, th […]

Citations

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CTCFBSDB institution(s)
Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN, USA
CTCFBSDB funding source(s)
Supported by the UT Center for Integrative and Translational Genomics; Department of Defense [W81XHW-05-01- 0227].

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