Long noncoding RNAs (lncRNAs) have emerged as key coordinators of biological and cellular processes. Characterizing lncRNA expression across cells and tissues is key to understanding their role in determining phenotypes, including human diseases. We present here FC-R2, a comprehensive expression atlas across a broadly defined human transcriptome, inclusive of over 109,000 coding and noncoding genes, as described in the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) study. This atlas greatly extends the gene annotation used in the original recount2 resource. We demonstrate the utility of the FC-R2 atlas by reproducing key findings from published large studies and by generating new results across normal and diseased human samples. In particular, we (a) identify tissue-specific transcription profiles for distinct classes of coding and noncoding genes, (b) perform differential expression analysis across thirteen cancer types, identifying novel noncoding genes potentially involved in tumor pathogenesis and progression, and (c) confirm the prognostic value for several enhancer lncRNAs expression in cancer. Our resource is instrumental for the systematic molecular characterization of lncRNA by the FANTOM6 Consortium. In conclusion, comprised of over 70,000 samples, the FC-R2 atlas will empower other researchers to investigate functions and biological roles of both known coding genes and novel lncRNAs.

中文翻译：

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重述 FANTOM CAGE 相关转录组。

长链非编码 RNA (lncRNA) 已成为生物和细胞过程的关键协调者。表征细胞和组织中的 lncRNA 表达是了解它们在确定表型（包括人类疾病）中的作用的关键。我们在此介绍 FC-R2，这是一个涵盖广泛定义的人类转录组的综合表达图谱，包括超过 109,000 个编码和非编码基因，如 FANTOM CAGE 相关转录组 (FANTOM-CAT) 研究中所述。这个图谱大大扩展了原始recount2 中使用的基因注释资源。我们通过复制已发表的大型研究的关键发现并通过在正常和患病人类样本中产生新结果来证明 FC-R2 图谱的实用性。特别是，我们 (a) 确定不同类别编码和非编码基因的组织特异性转录谱，(b) 对 13 种癌症类型进行差异表达分析，确定可能参与肿瘤发病机制和进展的新非编码基因，以及 (c)证实了癌症中几种增强子 lncRNA 表达的预后价值。我们的资源有助于 FANTOM6 联盟对 lncRNA 的系统分子表征。总之，由超过 70,000 个样本组成，