Allen Brain Atlas: Mouse gene expression data

These data were downloaded using python and the AllenSDK, and then imported and processed in Matlab. The dataset is a newer version of that analyzed in our paper: Fulcher, B. D. &amp; Fornito, A. A transcriptional signature of hub connectivity in the mouse connectome. <i>Proc. Natl. Acad. Sci. USA</i> <b>113</b>, 1435 (2016).<br>The data file, <b>AllenGeneDataset.mat</b>, contains gene expression data from 25469 section datasets, across 19419 genes, for 213 structures in the Allen Brain Atlas.The data is formatted in a Matlab structure with four components:<b><br></b><b>GeneExpData</b> contains fields for 'energy', 'density' (the expression energy and expression density of each section dataset), and also 'gene_energy' and 'gene_density' (the expression energy and density for each gene, after averaging across repeat section datasets)<br><br><b>sectionDatasetInfo</b> is a table that contains information about each section dataset: entrez_id of the gene, plane_of_section_id of the experiment (i.e., coronal, 1, or sagittal, 2), and the section_id. Each row labels columns of the 'energy' and 'density' matrices of GeneExpData.<br><br><b>geneInfo</b> contains information about each gene, with rows labeling the columns of the matrices in GeneExpData. Provides the acronym, entrez_id, gene_id, and name for each gene.<br><b>structInfo</b> labels the structure information for the 213 structures in the mesoscale mouse connectome reported by Oh, S. W. et al. A mesoscale connectome of the mouse brain. <i>Nature</i> <b>508</b>, 207 (2014). Each structure is labeled with its acronym, color_hex_triplet, id, name, and divisionLabel. Each row in this table corresponds to a row of the matrices in <b>GeneExpData</b>.<br><br>Note that ALL DATA in this repository were retrieved directly from the Allen Institute's API. If these data help you, then please acknowledge the amazing work and open science policies of the Allen Institute. For specific details of accreditation, please refer to the Allen Institute's citation policy if you use these data (link below).<br>Please contact me if you'd like any more information about how these data were put together. For example, if you'd like the raw files from the <b>allensdk</b> that haven't been processed in Matlab, or if you require more information about how the data were retrieved from the Allen SDK and processed using <b>Matlab</b>. I plan to make the code framework available on github when I find the time.

本数据集通过Python与AllenSDK下载获取，随后在Matlab中完成导入与处理工作。本数据集为本团队2016年发表于*美国国家科学院院刊*（*Proc. Natl. Acad. Sci. USA*）第113卷第1435页的论文《小鼠连接组枢纽连接的转录特征》（Fulcher, B. D. & Fornito, A. *A transcriptional signature of hub connectivity in the mouse connectome*）所分析数据集的更新版本。

数据文件**AllenGeneDataset.mat**包含艾伦脑图谱（Allen Brain Atlas）中213个脑区的基因表达数据，涵盖19419个基因的25469份切片数据集。该数据以Matlab结构体格式存储，包含四个组成部分：
**GeneExpData**：内含'energy'与'density'字段，分别对应单份切片数据集的表达能量与表达密度；同时设有'gene_energy'与'gene_density'字段，代表各基因在重复切片数据集取平均后的表达能量与密度。

**sectionDatasetInfo**：为一张数据表，记录每份切片数据集的相关信息：包括基因的Entrez ID、实验切片平面ID（冠状位为1，矢状位为2）以及切片ID。该表的每一行对应**GeneExpData**中'energy'与'density'矩阵的一列。

**geneInfo**：包含各基因的相关信息，其行对应**GeneExpData**中矩阵的列。该表为每个基因提供了基因缩写、Entrez ID、基因ID以及基因名称。

**structInfo**：记录了Oh等人2014年发表于*Nature*（*自然*）第508卷第207页的论文《小鼠脑介观连接组》（Oh, S. W. et al. *A mesoscale connectome of the mouse brain*）中所提及的213个脑区的结构信息。每个脑区均配有其缩写、color_hex_triplet、结构ID、脑区名称以及divisionLabel。该表的每一行对应**GeneExpData**中矩阵的一行。

请注意，本数据集仓库中的所有数据均直接从艾伦研究所（Allen Institute）的API接口获取。若本数据集对你的研究有所帮助，请致谢艾伦研究所的卓越工作与开放科学政策。若需了解具体的署名规范，请参考艾伦研究所的引用政策（链接见下文）。

若你需要了解本数据集的构建细节，可随时联系作者。例如，你可获取未经Matlab处理的AllenSDK原始文件，或了解更多关于从AllenSDK获取数据并通过Matlab处理的具体流程。本人将在闲暇时将代码框架上传至GitHub平台。