Over the past few years, with the rapid growth of deep-sequencing technology and the development of computational prediction algorithms, a large number of long non-coding RNAs (lncRNAs) have been identified in various types of human cancers. Therefore, it has become critical to determine how to properly annotate the potential function of lncRNAs from RNA-sequencing (RNA-seq) data and arrange the robust information and analysis into a useful system readily accessible by biological and clinical researchers. In order to produce a collective interpretation of lncRNA functions, it is necessary to integrate different types of data regarding the important functional diversity and regulatory role of these lncRNAs. In this study, we utilized transcriptomic sequencing data to systematically observe and identify lncRNAs and their potential functions from 5034 The Cancer Genome Atlas RNA-seq datasets covering 24 cancers. Then, we constructed the ‘lncExplore’ database that was developed to comprehensively integrate various types of genomic annotation data for collective interpretation. The distinctive features in our lncExplore database include (i) novel lncRNAs verified by both coding potential and translation efficiency score, (ii) pan-cancer analysis for studying the significantly aberrant expression across 24 human cancers, (iii) genomic annotation of lncRNAs, such as cis-regulatory information and gene ontology, (iv) observation of the regulatory roles as enhancer RNAs and competing endogenous RNAs and (v) the findings of the potential lncRNA biomarkers for the user-interested cancers by integrating clinical information and disease specificity score. The lncExplore database is to our knowledge the first public lncRNA annotation database providing cancer-specific lncRNA expression profiles for not only known but also novel lncRNAs, enhancer RNAs annotation and clinical analysis based on pan-cancer analysis. lncExplore provides a more complete pathway to highly efficient, novel and more comprehensive translation of laboratory discoveries into the clinical context and will assist in reinterpreting the biological regulatory function of lncRNAs in cancer research.

中文翻译：

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lncExplore：来自RNA测序数据的lncRNA的泛癌分析和系统功能注释数据库

近年来，随着深度测序技术的快速发展和计算预测算法的发展，大量的长链非编码RNA（lncRNAs）在各类人类癌症中被鉴定出来。因此，确定如何从 RNA 测序 (RNA-seq) 数据中正确注释 lncRNA 的潜在功能，并将稳健的信息和分析安排到一个生物和临床研究人员易于访问的有用系统中变得至关重要。为了产生对 lncRNA 功能的集体解释，有必要整合关于这些 lncRNA 的重要功能多样性和调节作用的不同类型的数据。在这项研究中，我们利用转录组测序数据从涵盖 24 种癌症的 5034 个癌症基因组图谱 RNA-seq 数据集中系统地观察和识别 lncRNA 及其潜在功能。然后，我们构建了“lncExplore”数据库，该数据库旨在全面整合各种类型的基因组注释数据以进行集体解释。我们的 lncExplore 数据库中的显着特征包括 (i) 通过编码潜力和翻译效率评分验证的新型 lncRNA，(ii) 用于研究 24 种人类癌症中显着异常表达的泛癌分析，(iii) lncRNA 的基因组注释，例如作为 我们构建了“lncExplore”数据库，该数据库旨在全面整合各种类型的基因组注释数据以进行集体解释。我们的 lncExplore 数据库中的显着特征包括 (i) 通过编码潜力和翻译效率评分验证的新型 lncRNA，(ii) 用于研究 24 种人类癌症中显着异常表达的泛癌分析，(iii) lncRNA 的基因组注释，例如作为 我们构建了“lncExplore”数据库，该数据库旨在全面整合各种类型的基因组注释数据以进行集体解释。我们的 lncExplore 数据库中的显着特征包括 (i) 通过编码潜力和翻译效率评分验证的新型 lncRNA，(ii) 用于研究 24 种人类癌症中显着异常表达的泛癌分析，(iii) lncRNA 的基因组注释，例如作为顺式调控信息和基因本体，(iv) 观察作为增强子 RNA 和竞争性内源性 RNA 的调控作用，以及 (v) 通过整合临床信息和疾病特异性评分，发现用户感兴趣的癌症的潜在 lncRNA 生物标志物。据我们所知，lncExplore 数据库是第一个公共 lncRNA 注释数据库，提供癌症特异性 lncRNA 表达谱，不仅用于已知的，而且还包括新的 lncRNA、增强子 RNA 注释和基于泛癌分析的临床分析。lncExplore 为将实验室发现高效、新颖和更全面地转化为临床环境提供了更完整的途径，并将有助于重新解释 lncRNA 在癌症研究中的生物学调节功能。