2014 | PETAR GLAŽAR, PANAGIOTIS PAPAVASILEIOU, and NIKOLAUS RAJEWSKY
circBase is a database and website for circular RNAs (circRNAs), providing access to merged and unified datasets of circRNAs and the evidence supporting their expression. The database allows users to search, download, and browse circRNA data within the genomic context. It also provides scripts to identify known and novel circRNAs in sequencing data. circBase is freely accessible at http://www.circbase.org/.
circRNAs are single-stranded RNA molecules that correspond to circular isoforms, often produced from exons with 5' and 3' ends covalently closed. They are highly stable and have specific spatiotemporal expression patterns. Although their function is unknown, circRNAs are interesting as potential biomarkers and for further research. circBase aims to serve the community by pooling and making accessible published data sets from different laboratories.
The database allows users to search circRNAs by identifiers, genomic location, sequence, gene description, or Gene Ontology term identifiers. It also provides a list search option for intersecting a large number of search terms with database contents and a table browser for conditional data retrieval. Search results are returned as a hyperlinked table, with additional information accessible via hyperlinks. circBase also allows users to export results in various formats, including comma-separated values (csv), tab-delimited text (tsv), and Excel Workbook (xlsx) formats.
circBase integrates data with external resources such as the UCSC Genome Browser and NCBI databases. It also enables users to interact with the database contents through a simple interface. The database currently hosts data from various organisms, including Homo sapiens, Mus musculus, Caenorhabditis elegans, and Latimeria samples. It does not cover viroids, which are already collected in other resources.
The database is implemented using HTML, CSS, and JavaScript, with data stored in a MySQL database. It is compatible with HTML5 and CSS3, and has been tested in Google Chrome 31.0, Mozilla Firefox 25.0, and Internet Explorer 10.0. circBase provides a single repository that collects, unifies, and annotates circRNA data in standardized formats. It extends public data sets with additional basic analysis and integrates this data with external resources. Users can interact with the database contents through a simple interface. The database is regularly updated with newly published data.circBase is a database and website for circular RNAs (circRNAs), providing access to merged and unified datasets of circRNAs and the evidence supporting their expression. The database allows users to search, download, and browse circRNA data within the genomic context. It also provides scripts to identify known and novel circRNAs in sequencing data. circBase is freely accessible at http://www.circbase.org/.
circRNAs are single-stranded RNA molecules that correspond to circular isoforms, often produced from exons with 5' and 3' ends covalently closed. They are highly stable and have specific spatiotemporal expression patterns. Although their function is unknown, circRNAs are interesting as potential biomarkers and for further research. circBase aims to serve the community by pooling and making accessible published data sets from different laboratories.
The database allows users to search circRNAs by identifiers, genomic location, sequence, gene description, or Gene Ontology term identifiers. It also provides a list search option for intersecting a large number of search terms with database contents and a table browser for conditional data retrieval. Search results are returned as a hyperlinked table, with additional information accessible via hyperlinks. circBase also allows users to export results in various formats, including comma-separated values (csv), tab-delimited text (tsv), and Excel Workbook (xlsx) formats.
circBase integrates data with external resources such as the UCSC Genome Browser and NCBI databases. It also enables users to interact with the database contents through a simple interface. The database currently hosts data from various organisms, including Homo sapiens, Mus musculus, Caenorhabditis elegans, and Latimeria samples. It does not cover viroids, which are already collected in other resources.
The database is implemented using HTML, CSS, and JavaScript, with data stored in a MySQL database. It is compatible with HTML5 and CSS3, and has been tested in Google Chrome 31.0, Mozilla Firefox 25.0, and Internet Explorer 10.0. circBase provides a single repository that collects, unifies, and annotates circRNA data in standardized formats. It extends public data sets with additional basic analysis and integrates this data with external resources. Users can interact with the database contents through a simple interface. The database is regularly updated with newly published data.