Abstract

Accumulated evidence suggests that the widely expressed long-non-coding RNAs (lncRNAs) are involved in biogenesis. Some aberrant lncRNAs are closely related to pathological changes, for instance, in cancer. Both in tumorigenesis and cancer progression, depending on the interplay with cellular molecules, lncRNAs can modulate transcriptional interference, chromatin remodeling, post-translational regulation and protein modification, and further interfere with signaling pathways. Aiming to the diagnosis/ prognosis markers or potential therapeutical targets, it is important to figure out the specific mechanism and the tissue-specific expressing patterns of lncRNAs. Generally, the bioinformatics analysis is the first step. More and more in silico databases are increasing. But the existing integrative online platforms’ functions are not only having their unique features but also share some common features, which may lead to a waste of time for researchers. Here, we reviewed these web tools according to the functions. For each database, we clarified the data source, analysis method and the evidence that the analysis result is derived from. This review also illustrated examples in practical use for a specific lncRNA by these web tools. It will provide convenience for researchers to quickly choose the appropriate bioinformatics web tools in oncology studies.

中文翻译：

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在肿瘤学研究中执行长非编码 RNA 分析的网络工具

摘要

积累的证据表明，广泛表达的长链非编码 RNA (lncRNA) 参与生物发生。一些异常的 lncRNA 与病理变化密切相关，例如在癌症中。在肿瘤发生和癌症进展中，lncRNAs 可以通过与细胞分子的相互作用调节转录干扰、染色质重塑、翻译后调控和蛋白质修饰，并进一步干扰信号通路。针对诊断/预后标志物或潜在的治疗靶点，弄清楚lncRNA的具体机制和组织特异性表达模式非常重要。通常，生物信息学分析是第一步。越来越多的计算机数据库正在增加。但是现有的综合性在线平台的功能不仅有其独特之处，而且还具有一些共性，这可能会浪费研究人员的时间。在这里，我们根据功能回顾了这些网络工具。对于每个数据库，我们明确了数据来源、分析方法和分析结果的依据。这篇综述还举例说明了这些网络工具对特定 lncRNA 的实际使用示例。它将为研究人员在肿瘤学研究中快速选择合适的生物信息学网络工具提供便利。