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A complete list of the sources used to curate the CTCF binding sites within the database can be found on the Help page. Download Download binding sites: How to cite the CTCFBSDB database Ziebarth JD, Bhattacharya A, Cui Y (2013) CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization. Nucleic Acids Research. 41(D1):D188-D194.

The sequences of CTCF-binding sites in the database vary from 20 bp to several hundred bp. There are two reasons for this length heterogeneity. First, different experimental methods may have different basepair resolutions for locating CTCF-binding sites. Second, different laboratories often have different research goals when they publish the ...

We have constructed a CTCF-binding site database (CTCFBSDB) to characterize experimentally identified and computationally predicted CTCF-binding sties. Biological knowledge and data from multiple resources have been integrated into the database, including sequence data, genetic polymorphisms, function annotations, histone methylation profiles ...

To reflect this important progress, we have integrated CTCF-binding sites with genomic topological domains defined using Hi-C data. Additionally, the updated database includes new features enabled by new CTCF-binding site data, including binding site occupancy and the ability to visualize overlapping CTCF-binding sites determined in separate ...

We find that gain of CTCF binding in cancer associates with increased chromatin interactions and cancer-specific gene activation, while loss of CTCF binding occurred at promoters of genes present with lower expression in cancer compared to normal cells. Our results substantiate CTCF binding alteration as a functional epigenomic signature of cancer.

Screenshot of an example webpage for a CTCF-binding sequence (ENCODE_OC_hg18_MCF-7_744758) in CTCFBSDB 2.0. The database provides a description of the binding site, where the binding sequence is located within topological domains, and a Genome Browser viewer showing the genomic context of the binding site.

This track was produced as part of the ENCODE Project. This track displays maps of genome-wide binding of the CTCF transcription factor in different cell lines using ChIP-seq high-throughput sequencing. Display Conventions and Configuration. This track is a multi-view composite track that contains multiple data types (views). For each view ...

The diversity of CTCF binding motifs has led to a fragmented landscape of CTCF binding data. We collected position weight matrices of CTCF binding motifs and defined strand-oriented CTCF binding sites in the human and mouse genomes, including the recent Telomere to Telomere and mm39 assemblies.

Each CTCF binding site in the database is annotated with data collected from multiple resources that is displayed on the main record page of that binding site. This page is organized into the following sections: (1) Description: A table containing general information about the binding site and its potential functional significance.

The diversity of CTCF binding motifs has led to a fragmented landscape of CTCF binding data. We collected position weight matrices of CTCF binding motifs and defined strand-oriented CTCF binding sites in the human and mouse genomes, including the recent Telomere to Telomere and mm39 assemblies. We included selected experimentally determined and ...

Additionally, the updated database includes new features enabled by new CTCF-binding site data, including binding site occupancy and the ability to visualize overlapping CTCF-binding sites determined in separate experiments. Consortium data used in this publication ENCODE TF ChIP, mouse TF CHIP, DNA methylation, Fig 1-3.

Co-oriented CTCF binding sites are notably enriched at the anchor points of these loops across various cell types [34,35,36]. Therefore, we leverage the spatial information of potential loop anchors provided by CTCF binding regions obtained from CTCF ChIP-seq data to enhance the identification of chromatin loops.

CTCF-binding sites were found to be commonly distributed along the vertebrate genomes. We have constructed a CTCF-binding site database (CTCFBSDB) to characterize experimentally identified and computationally predicted CTCF-binding sties. Biological knowledge and data from multiple resources have been integrated into the database, including ...

Identification of CTCF-binding sequences that overlap a given CTCF-binding sequence: the database now contains CTCF-binding sites identified in many tissues and cell types in mice and humans, making it possible to investigate if CTCF binding is specific to a particular cell type or conserved and, potentially, help limit the location of a ...

Screenshot of an example webpage for a CTCF-binding sequence (ENCODE_OC_hg18_MCF-7_744758) in CTCFBSDB 2.0. The database provides a description of the binding site, where the binding sequence is ...

CTCFBSDB 2.0: A database for CTCF binding sites and genome organization Home. Search Experimentally Identified CTCFBS: Browse Topological Domain: Predicted CTCFBS: CTCFBS Prediction Tool: Help : Range Search : Select Data to search: Species: Data Source: OR Select Reference by PMID or ENCODE File: ...

there is a CTCF-binding site motif that is highly conserved in vertebrates (5). Initial consensus CTCF-binding site motifs were then used to computationally predict CTCF-binding sites (5,6). Within this context, we introduced the first public database of CTCF-binding sites, CTCFBSDB, in 2007 (10). The initial version of CTCFBSDB contained ...

CTCFBSDB 2.0: A database for CTCF binding sites and genome organization : Home. Search Experimentally Identified CTCFBS: Browse Topological Domain: Predicted CTCFBS: CTCFBS Prediction Tool: Help : Species: Cell Type: Chromosome: Total 371 records ...

CTCFBSDB 2.0: A database for CTCF binding sites and genome organization : Home. Search Experimentally Identified CTCFBS: Browse Topological Domain: Predicted CTCFBS: CTCFBS Prediction Tool: Help : Scan sequences for the single best match to CTCF position weight matrices Enter your sequence here: (in fasta format)

CTCFBSDB 2.0: A database for CTCF binding sites and genome organization Home. Search Experimentally Identified CTCFBS: Browse Topological Domain: Predicted CTCFBS: CTCFBS Prediction Tool: Help : Species Sequence Chromosome Location 5' Flanking Gene 3' Flanking Gene Total ...