| URL: | http://geneyun.net/CSCD2 |
| Full name: | cancer-specific circRNA database |
| Description: | CSCD collects available RNASeq datasets in cancer and normal samples, and provides an integrated circRNA database to benefit functional studies of cancer-specific circRNAs. CSCD also collects normal and common circRNAs, which allow users for other studies. For example, users can compare circRNAs in their cancer samples with CSCD to examine whether those circRNAs are cancer-specific or not. Users can view the potential functional regulation and translation on these circRNAs through prediction of MRE, RNA binding protein and open reading frame. |
| Year founded: | 2018 |
| Last update: | |
| Version: | V2.0 |
| Accessibility: | |
| Country/Region: | China |
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| University/Institution: | Wuhan University |
| Address: | School of Basic Medical Sciences, Wuhan University Tel: +86 27 6875 9702; Fax: +86 27 6875 9702 |
| City: | Wuhan |
| Province/State: | Hubei |
| Country/Region: | China |
| Contact name (PI/Team): | Chunjiang He |
| Contact email (PI/Helpdesk): | che@whu.edu.cn |
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CSCD2: an integrated interactional database of cancer-specific circular RNAs. [PMID: 34551437]
The significant function of circRNAs in cancer was recognized in recent work, so a well-organized resource is required for characterizing the interactions between circRNAs and other functional molecules (such as microRNA and RNA-binding protein) in cancer. We previously developed cancer-specific circRNA database (CSCD), a comprehensive database for cancer-specific circRNAs, which is widely used in circRNA research. Here, we updated CSCD to CSCD2 (http://geneyun.net/CSCD2 or http://gb.whu.edu.cn/CSCD2), which includes significantly more cancer-specific circRNAs identified from a large number of human cancer and normal tissues/cell lines. CSCD2 contains >1000 samples (825 tissues and 288 cell lines) and identifies a large number of circRNAs: 1 013 461 cancer-specific circRNAs, 1 533 704 circRNAs from only normal samples and 354 422 circRNAs from both cancer and normal samples. In addition, CSCD2 predicts potential miRNA-circRNA and RBP-circRNA interactions using binding motifs from >200 RBPs and 2000 microRNAs. Furthermore, the potential full-length and open reading frame sequence of these circRNAs were also predicted. Collectively, CSCD2 provides a significantly enhanced resource for exploring the function and regulation of circRNAs in cancer. |
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CSCD: a database for cancer-specific circular RNAs. [PMID: 29036403]
Circular RNA (circRNA) is a large group of RNA family extensively existed in cells and tissues. High-throughput sequencing provides a way to view circRNAs across different samples, especially in various diseases. However, there is still no comprehensive database for exploring the cancer-specific circRNAs. We collected 228 total RNA or polyA(-) RNA-seq samples from both cancer and normal cell lines, and identified 272 152 cancer-specific circRNAs. A total of 950 962 circRNAs were identified in normal samples only, and 170 909 circRNAs were identified in both tumor and normal samples, which could be further used as non-tumor background. We constructed a cancer-specific circRNA database (CSCD, http://gb.whu.edu.cn/CSCD). To understand the functional effects of circRNAs, we predicted the microRNA response element sites and RNA binding protein sites for each circRNA. We further predicted potential open reading frames to highlight translatable circRNAs. To understand the association between the linear splicing and the back-splicing, we also predicted the splicing events in linear transcripts of each circRNA. As the first comprehensive cancer-specific circRNA database, we believe CSCD could significantly contribute to the research for the function and regulation of cancer-associated circRNAs. |