Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China.
Department of Pathophysiology, School of Medicine, Southeast University, Nanjing 210009, China.
Genomics Proteomics Bioinformatics. 2023 Apr;21(2):278-282. doi: 10.1016/j.gpb.2022.09.004. Epub 2022 Sep 23.
Ferroptosis is a form of regulated cell death driven by the accumulation of lipid hydroperoxides. Regulation of ferroptosis might be beneficial to cancer treatment. Non-coding RNAs (ncRNAs) are a class of RNA transcripts that generally cannot encode proteins and have been demonstrated to play critical roles in regulating ferroptosis. Herein, we developed ncFO, the ncRNA-ferroptosis association database, to document the manually curated and predicted ncRNAs that are associated with ferroptosis. Collectively, ncFO contains 90 experimentally verified entries, including 46 microRNAs (miRNAs), 21 long non-coding RNAs (lncRNAs), and 17 circular RNAs (circRNAs). In addition, ncFO also incorporates two online prediction tools based on the regulation and co-expression of ncRNA and ferroptosis genes. Using default parameters, we obtained 3260 predicted entries, including 598 miRNAs and 178 lncRNAs, by regulation, as well as 2,592,661 predicted entries, including 967 miRNAs and 9632 lncRNAs, by ncRNA-ferroptosis gene co-expression in more than 8000 samples across 20 cancer types. The detailed information of each entry includes ncRNA name, disease, species, tissue, target, regulation, publication time, and PubMed identifier. ncFO also provides survival analysis and differential expression analysis for ncRNAs. In summary, ncFO offers a user-friendly platform to search and predict ferroptosis-associated ncRNAs, which might facilitate research on ferroptosis and discover potential targets for cancer treatment. ncFO can be accessed at http://www.jianglab.cn/ncFO/.
铁死亡是一种受脂质氢过氧化物积累驱动的调控细胞死亡形式。铁死亡的调控可能对癌症治疗有益。非编码 RNA(ncRNA)是一类通常不能编码蛋白质的 RNA 转录物,已被证明在调控铁死亡中发挥关键作用。在此,我们开发了 ncFO,即非编码 RNA-铁死亡关联数据库,以记录与铁死亡相关的经过人工 curated 和预测的 ncRNA。总的来说,ncFO 包含 90 个经过实验验证的条目,包括 46 个 microRNAs(miRNAs)、21 个长非编码 RNA(lncRNAs)和 17 个环状 RNA(circRNAs)。此外,ncFO 还整合了两个基于 ncRNA 和铁死亡基因的调控和共表达的在线预测工具。使用默认参数,我们通过调控获得了 3260 个预测条目,包括 598 个 miRNAs 和 178 个 lncRNAs,以及通过 ncRNA-铁死亡基因在超过 8000 个样本中的共表达获得了 2592661 个预测条目,包括 967 个 miRNAs 和 9632 个 lncRNAs。在 20 种癌症类型中。每个条目的详细信息包括 ncRNA 名称、疾病、物种、组织、靶标、调控、发表时间和 PubMed 标识符。ncFO 还提供了 ncRNA 的生存分析和差异表达分析。总之,ncFO 提供了一个用户友好的平台,用于搜索和预测与铁死亡相关的 ncRNA,这可能有助于铁死亡的研究并发现癌症治疗的潜在靶点。ncFO 可在 http://www.jianglab.cn/ncFO/ 访问。