| URL: | http://circatlas.biols.ac.cn |
| Full name: | An integrated resource of circRNAs in vertebrates |
| Description: | circAtlas 2.0 integrates millions of circRNAs across 7 species (human, macaca, mouse, rat, pig, chicken, dog) and a variety of tissues. The circAtlas 2.0 can fill this gap by integrating the most comprehensive circRNAs and their expression and functional profiles in vertebrates, which provides a foundation for circRNA studies and serves as a powerful starting point to investigate their biological significance. |
| Year founded: | 2020 |
| Last update: | |
| Version: | v2.0 |
| Accessibility: |
Manual:
Accessible
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| Country/Region: | China |
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| Data object: | |
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| University/Institution: | Beijing Institutes of Life Science, Chinese Academy of Sciences |
| Address: | |
| City: | Beijing |
| Province/State: | Beijing |
| Country/Region: | China |
| Contact name (PI/Team): | Fangqing Zhao |
| Contact email (PI/Helpdesk): | zhfq@biols.ac.cn |
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circAtlas 3.0: a gateway to 3 million curated vertebrate circular RNAs based on a standardized nomenclature scheme. [PMID: 37739414]
Recent studies have demonstrated the important regulatory role of circRNAs, but an in-depth understanding of the comprehensive landscape of circRNAs across various species still remains unexplored. The current circRNA databases are often species-restricted or based on outdated datasets. To address this challenge, we have developed the circAtlas 3.0 database, which contains a rich collection of 2674 circRNA sequencing datasets, curated to delineate the landscape of circRNAs within 33 distinct tissues spanning 10 vertebrate species. Notably, circAtlas 3.0 represents a substantial advancement over its precursor, circAtlas 2.0, with the number of cataloged circRNAs escalating from 1 007 087 to 3 179 560, with 2 527 528 of them being reconstructed into full-length isoforms. circAtlas 3.0 also introduces several notable enhancements, including: (i) integration of both Illumina and Nanopore sequencing datasets to detect circRNAs of extended lengths; (ii) employment of a standardized nomenclature scheme for circRNAs, providing information of the host gene and full-length circular exons; (iii) inclusion of clinical cancer samples to explore the biological function of circRNAs within the context of cancer and (iv) links to other useful resources to enable user-friendly analysis of target circRNAs. The updated circAtlas 3.0 provides an important platform for exploring the evolution and biological implications of vertebrate circRNAs, and is freely available at http://circatlas.biols.ac.cn and https://ngdc.cncb.ac.cn/circatlas. |
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CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. [PMID: 32345360]
Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-depth information for candidate circRNA prioritization. To address this, we integrate circular transcript collections to develop the circAtlas database based on 1070 RNA-seq samples collected from 19 normal tissues across six vertebrate species. This database contains 1,007,087 highly reliable circRNAs, of which over 81.3% have been assembled into full-length sequences. We profile their expression pattern, conservation, and functional annotation. We describe a novel multiple conservation score, co-expression, and regulatory networks for circRNA annotation and prioritization. CircAtlas can be accessed at http://circatlas.biols.ac.cn/. |