School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China.
Hubei Province Key Laboratory of Allergy and Immunology, Wuhan 430071, Hubei, China.
Nucleic Acids Res. 2018 Jan 4;46(D1):D925-D929. doi: 10.1093/nar/gkx863.
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.
环状 RNA（circRNA）是细胞和组织中广泛存在的一类大型 RNA 家族。高通量测序为在不同样本中观察 circRNAs 提供了一种方法，特别是在各种疾病中。然而，目前仍然没有一个全面的数据库来探索癌症特异性 circRNAs。我们收集了来自癌症和正常细胞系的 228 个总 RNA 或 polyA(-) RNA-seq 样本，并鉴定了 272152 个癌症特异性 circRNAs。在正常样本中总共鉴定了 950962 个 circRNAs，在肿瘤和正常样本中鉴定了 170909 个 circRNAs，可以进一步作为非肿瘤背景使用。我们构建了一个癌症特异性 circRNA 数据库（CSCD，http://gb.whu.edu.cn/CSCD）。为了了解 circRNAs 的功能影响，我们预测了每个 circRNA 的 microRNA 反应元件位点和 RNA 结合蛋白位点。我们进一步预测了潜在的开放阅读框，以突出可翻译的 circRNAs。为了了解线性剪接和反向剪接之间的关联，我们还预测了每个 circRNA 的线性转录本中的剪接事件。作为第一个全面的癌症特异性 circRNA 数据库，我们相信 CSCD 将为研究癌症相关 circRNAs 的功能和调控做出重大贡献。
