Noncoding RNAs (ncRNAs) play critical roles in many critical biological processes and have become a novel class of potential targets and bio-markers for disease diagnosis, therapy, and prognosis. Annotating and analysing ncRNA-disease association data are essential but challenging. Current computational resources lack comprehensive database platforms to consistently interpret and prioritize ncRNA-disease association data for biomedical investigation and application. Here, we present the ncRPheno database platform (http://lilab2.sysu.edu.cn/ncrpheno), which comprehensively integrates and annotates ncRNA-disease association data and provides novel searches, visualizations, and utilities for association identification and validation. ncRPheno contains 482,751 non-redundant associations between 14,494 ncRNAs and 3,210 disease phenotypes across 11 species with supporting evidence in the literature. A scoring model was refined to prioritize the associations based on evidential metrics. Moreover, ncRPheno provides user-friendly web interfaces, novel visualizations, and programmatic access to enable easy exploration, analysis, and utilization of the association data. A case study through ncRPheno demonstrated a comprehensive landscape of ncRNAs dysregulation associated with 22 cancers and uncovered 821 cancer-associated common ncRNAs. As a unique database platform, ncRPheno outperforms the existing similar databases in terms of data coverage and utilities, and it will assist studies in encoding ncRNAs associated with phenotypes ranging from genetic disorders to complex diseases.

Abbreviations

APIs: application programming interfaces; circRNA: circular RNA; ECO: Evidence & Conclusion Ontology; EFO: Experimental Factor Ontology; FDR: false discovery rate; GO: Gene Ontology; GWAS: genome wide association studies; HPO: Human Phenotype Ontology; ICGC: International Cancer Genome Consortium; lncRNA: long noncoding RNA; miRNA: micro RNA; ncRNA: noncoding RNA; NGS: next generation sequencing; OMIM: Online Mendelian Inheritance in Man; piRNA: piwi-interacting RNA; snoRNA: small nucleolar RNA; TCGA: The Cancer Genome Atlas

中文翻译：

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ncRPheno：用于识别和验证疾病相关非编码 RNA 的综合数据库平台。

非编码RNA（ncRNA）在许多关键的生物过程中发挥着关键作用，并已成为疾病诊断、治疗和预后的一类新型潜在靶点和生物标志物。注释和分析 ncRNA-疾病关联数据至关重要，但也具有挑战性。当前的计算资源缺乏全面的数据库平台来一致地解释和优先考虑用于生物医学研究和应用的 ncRNA 疾病关联数据。在这里，我们提出了 ncRPheno 数据库平台（http://lilab2.sysu.edu.cn/ncrpheno），该平台全面集成和注释 ncRNA-疾病关联数据，并提供新颖的搜索、可视化以及用于关联识别和验证的实用程序。ncRPheno 包含 11 个物种的 14,494 个 ncRNA 与 3,210 个疾病表型之间的 482,751 个非冗余关联，并有文献支持证据。评分模型经过改进，可以根据证据指标对关联进行优先级排序。此外，ncRPheno 提供用户友好的 Web 界面、新颖的可视化和编程访问，以便轻松探索、分析和利用关联数据。通过 ncRPheno 进行的案例研究展示了与 22 种癌症相关的 ncRNA 失调的全面情况，并发现了 821 种与癌症相关的常见 ncRNA。作为一个独特的数据库平台，ncRPheno 在数据覆盖范围和实用性方面优于现有的类似数据库，它将有助于编码与从遗传性疾病到复杂疾病等表型相关的 ncRNA 的研究。

缩写

API：应用程序编程接口；circRNA：环状RNA；ECO：证据与结论本体论；EFO：实验因素本体；FDR：错误发现率；GO：基因本体论；GWAS：全基因组关联研究；HPO：人类表型本体论；ICGC：国际癌症基因组联盟；lncRNA：长非编码RNA；miRNA：微小RNA；ncRNA：非编码RNA；NGS：下一代测序；OMIM：在线人类孟德尔遗传；piRNA：piwi 相互作用 RNA；snoRNA：核仁小RNA；TCGA：癌症基因组图谱