Abugessaisa Imad, Noguchi Shuhei, Carninci Piero, Kasukawa Takeya
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
Methods Mol Biol. 2017;1611:199-217. doi: 10.1007/978-1-4939-7015-5_15.
The Functional Annotation of the Mammalian Genome 5 (FANTOM5) project conducted transcriptome analysis of various mammalian cell types and provided a comprehensive resource to understand transcriptome and transcriptional regulation in individual cellular states encoded in the genome.FANTOM5 used cap analysis of gene expression (CAGE) with single-molecule sequencing to map transcription start sites (TSS) and measured their expression in a diverse range of samples. The main results from FANTOM5 were published as a promoter-level mammalian expression atlas and an atlas of active enhancers across human cell types. The FANTOM5 dataset is composed of raw experimental data and the results of bioinformatics analyses. In this chapter, we give a detailed description of the content of the FANTOM5 dataset and elaborate on different computing applications developed to publish the data and enable reproducibility and discovery of new findings. We present use cases in which the FANTOM5 dataset has been reused, leading to new findings.
哺乳动物基因组功能注释5（FANTOM5）项目对多种哺乳动物细胞类型进行了转录组分析，并提供了一个全面的资源，以了解基因组中编码的个体细胞状态下的转录组和转录调控。FANTOM5使用基因表达帽分析（CAGE）和单分子测序来绘制转录起始位点（TSS），并在各种样本中测量它们的表达。FANTOM5的主要结果作为启动子水平的哺乳动物表达图谱和跨人类细胞类型的活性增强子图谱发表。FANTOM5数据集由原始实验数据和生物信息学分析结果组成。在本章中，我们详细描述了FANTOM5数据集的内容，并阐述了为发布数据以及实现可重复性和发现新发现而开发的不同计算应用程序。我们展示了FANTOM5数据集被重新使用并产生新发现的用例。
