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. & Fornito, A. A transcriptional signature of hub connectivity in the mouse connectome. Proc. Natl. Acad. Sci. USA 113, 1435 (2016).The data file, AllenGeneDataset.mat, 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:GeneExpData 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)sectionDatasetInfo 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.geneInfo 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.structInfo 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. Nature 508, 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 GeneExpData.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).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 allensdk 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 Matlab. 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环境中完成导入与处理工作。本数据集为我们团队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《小鼠连接组中枢连接的转录特征》（A transcriptional signature of hub connectivity in the mouse connectome，作者：Fulcher, B. D. & Fornito, A.）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个脑结构的基因表达数据，涵盖19419个基因的25469个切片数据集。
该数据以Matlab结构体格式存储，包含四个组成部分：
1. GeneExpData：包含'energy'、'density'字段（分别对应各切片数据集的表达能量与表达密度），以及'gene_energy'、'gene_density'字段（分别为重复切片数据集取平均后，单个基因的表达能量与密度）。
2. sectionDatasetInfo：一张数据表，收录各切片数据集的相关信息，包括基因的Entrez ID、实验的切片平面编号（冠状面为1，矢状面为2）以及切片ID。该数据表的每一行对应GeneExpData中'energy'与'density'矩阵的列。
3. geneInfo：收录各基因的相关信息，其行对应GeneExpData内各矩阵的列，为每个基因提供缩写、Entrez ID、基因ID以及基因名称。
4. structInfo：收录Oh, S. W. 等人2014年发表于《自然》（Nature）第508卷第207页的论文《小鼠脑介观连接组》（A mesoscale connectome of the mouse brain）中提及的213个脑结构的信息。每个脑结构配有其缩写、color_hex_triplet（十六进制颜色三元组）、id、名称以及divisionLabel（分区标签）。该数据表的每一行对应GeneExpData内各矩阵的行。
请注意，本仓库内所有数据均直接从艾伦研究所（Allen Institute）的API接口获取。若本数据集为你的研究提供了帮助，请致谢艾伦研究所的开创性工作与开放科学政策。如需了解具体的署名规范，请在使用本数据集时参考艾伦研究所的引用政策（链接见下方）。
若你需要更多关于本数据集构建细节的信息，例如获取未经Matlab处理的AllenSDK原始文件，或是需要了解更多从Allen SDK获取数据并在Matlab中完成处理的具体流程，请随时与我联系。我将在后续抽空将代码框架上传至GitHub平台。