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2022, Genomics, Proteomics & Bioinformatics. DOI: 10.1016/j.gpb.2022.09.004
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis
Shunheng Zhou , Yu-e Huang , Jiani Xing , Xu Zhou , Sina Chen , Jiahao Chen , Lihong Wang , Wei Jiang
Abstract:
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 (PMID). 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/.
2022-10-31 21:19:00
#paper doi:10.1016/j.gpb.2022.09.004. ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis. Genomics Proteomics Bioinformatics. 2022. 细胞死亡在组织发育和体内平衡中起关键作用,并抑制癌细胞的过度增殖。铁死亡是由脂质过氧化诱导的一种特殊类型的调节性细胞死亡方式,探索铁死亡的潜在调节因子将有助于阐明其分子机制和仔细研究潜在的药物靶点。 目前虽然有铁死亡与疾病关联的调节剂和标志物数据库FerrD,但不便于研究人员对铁死亡相关非编码RNA(ncRNA,包括miRNA、lncRNA、circRNA)进行系统研究,ncRNA已被证实参与铁死亡的调节,文献中的信息不方便研究人员从综合角度表征铁死亡相关的ncRNA。为了填补这一空白,作者开发了ncRNA-铁死亡关联数据库(ncFO, http://www.jianglab.cn/ncFO/),ncFO是第一个收集了实验验证的铁死亡相关ncRNA并预测候选ncRNA-铁死亡关联的平台。用户可以获得经过实验验证的ncRNA-铁死亡关联,包括ncRNA名称、疾病、物种、组织、靶标、调控、发表时间和PMID。此外,ncFO数据库还提供了ncRNA的生存分析和差异表达分析。数据库为查询和分析铁死亡相关的ncRNA提供可靠的分析平台,为癌症治疗靶点的识别提供参考。
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