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Towards a comprehensive pipeline to identify and functionally annotate long noncoding RNA (lncRNA)
Computers in Biology and Medicine ( IF 7.7 ) Pub Date : 2020-10-13 , DOI: 10.1016/j.compbiomed.2020.104028
Yashpal Ramakrishnaiah 1 , Levin Kuhlmann 2 , Sonika Tyagi 3
Affiliation  

Long noncoding RNAs (lncRNAs) are implicated in various genetic diseases and cancer, attributed to their critical role in gene regulation. They are a divergent group of RNAs and are easily differentiated from other types with unique characteristics, functions, and mechanisms of action. In this review, we provide a list of some of the prominent data repositories containing lncRNAs, their interactome, and predicted and validated disease associations. Next, we discuss various wet-lab experiments formulated to obtain the data for these repositories. We also provide a critical review of in silico methods available for the identification purpose and suggest techniques to further improve their performance. The bulk of the methods currently focus on distinguishing lncRNA transcripts from the coding ones. Functional annotation of these transcripts still remains a grey area and more efforts are needed in that space. Finally, we provide details of current progress, discuss impediments, and illustrate a roadmap for developing a generalized computational pipeline for comprehensive annotation of lncRNAs, which is essential to accelerate research in this area.



中文翻译:

建立全面的流程以识别和功能注释长的非编码RNA(lncRNA)

长非编码RNA(lncRNA)与多种遗传疾病和癌症有关,这归因于它们在基因调控中的关键作用。它们是不同的RNA组,很容易与其他类型的RNA区别开来,具有独特的特征,功能和作用机制。在这篇综述中,我们提供了一些包含lncRNA,其相互作用基因组以及预测和验证的疾病关联的重要数据库的列表。接下来,我们讨论为获得这些存储库的数据而制定的各种湿实验室实验。我们还提供对计算机技术的严格审查可用于识别目的的方法,并建议进一步改善其性能的技术。目前,大多数方法集中于区分lncRNA转录本和编码转录本。这些成绩单的功能注释仍是一个灰色区域,在该领域需要更多的努力。最后,我们提供了当前进展的细节,讨论了障碍,并说明了开发用于lncRNA的全面注释的通用计算管道的路线图,这对于加快该领域的研究至关重要。

更新日期:2020-10-30
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