<strong>Dataset for exploring genomic-epigenetic configurations in lung adenocarcinoma without clinically actionable genetic alterations </strong>

The purpose of this figshare is to make available all data from the peak-to-gene links analysis presented in Kaneko S. et al., "Mechanism of<em> ERBB2</em> gene overexpression by the formation of super-enhancer with genomic structural abnormalities in lung adenocarcinoma without clinically actionable genetic alterations", as well as files for genome-wide visualization of ChIP-seq and Hi-C datasets. The ChIP-seq and Hi-C data file formats are as follows: The bigWig format is used in ChIP-seq studies for efficient storage and visualization of the genomic locations of the H3K27Ac modification. These files can be easily loaded into genome browsers like the Integrative Genomics Viewer (IGV) [1], allowing for interactive exploration and visualization of these active enhancer and promoter regions. The mcool file format is a specialized file type used to visualize and analyze Hi-C data. Hi-C is a technique for investigating chromatin interactions within the genome, and its results generate complex and large-scale datasets that require specialized formats for efficient management and manipulation. "mcool" stands for "multi-resolution cooler," and it contains multiple "resolutions" or levels of detail for the same Hi-C dataset. These resolutions represent different degrees of binning of the original Hi-C interaction matrix. This multi-resolution format allows efficient zooming and panning across different scales when visualizing Hi-C data in genome browsers such as HiGlass [2]. <br> References 1. Thorvaldsdottir H, Robinson JT, Mesirov JP: Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. <em>Brief Bioinform </em>2013, 14:178-192. 2. Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Azhir A, Kumar N, et al: HiGlass: web-based visual exploration and analysis of genome interaction maps. <em>Genome Biol </em>2018, 19:125.本figshare数据集仓库旨在公开Kaneko S.等人发表于论文《无临床可操作遗传改变的肺腺癌中，通过基因组结构异常形成超级增强子介导ERBB2基因过表达的机制》中的全部峰-基因关联分析数据，以及用于全基因组可视化的染色质免疫共沉淀测序（ChIP-seq）和Hi-C数据集文件。 ChIP-seq与Hi-C数据的文件格式说明如下： 在染色质免疫共沉淀测序（ChIP-seq）研究中，采用bigWig格式实现H3K27Ac修饰基因组位置信息的高效存储与可视化。此类文件可便捷加载至整合基因组浏览器（Integrative Genomics Viewer，简称IGV）[1]等基因组浏览器中，实现活性增强子与启动子区域的交互式探索与可视化。 mcool格式是专为Hi-C数据可视化与分析开发的专用文件类型。Hi-C技术用于探究基因组内的染色质相互作用，其产出的数据规模庞大且结构复杂，需采用专用格式实现高效管理与操作。“mcool”为“多分辨率cooler”的缩写，其包含同一Hi-C数据集的多种分辨率或细节层级，这些分辨率对应原始Hi-C相互作用矩阵的不同分箱程度。该多分辨率格式可实现在HiGlass[2]等基因组浏览器中可视化Hi-C数据时，跨不同尺度高效缩放与平移。 参考文献 1. Thorvaldsdottir H, Robinson JT, Mesirov JP：整合基因组浏览器（IGV）：高性能基因组数据可视化与探索工具. 《生物信息学简报》（Brief Bioinform）2013, 14:178-192. 2. Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Azhir A, Kumar N, 等：HiGlass：基于网页的基因组相互作用图谱可视化探索与分析工具. 《基因组生物学》（Genome Biol）2018, 19:125.