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（艾伦软件开发工具包）下载，随后在Matlab中完成导入与处理。该数据集为我们2016年发表于《美国国家科学院院刊》（Proc. Natl. Acad. Sci. USA）的论文《小鼠连接组中枢纽连接的转录组特征》（作者：Fulcher, B. D. & Fornito, A.）所分析数据集的更新版本，原文刊于第113卷，第1435页。

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、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：
1. GeneExpData：包含'energy'（表达能量）与'density'（表达密度）字段，对应每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，为各基因在重复切片数据集上取平均后的表达能量与密度。
2. sectionDatasetInfo：为每张切片数据集的信息表，包含对应基因的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'矩阵的列索引。
3. geneInfo：包含各基因的相关信息，表行对应GeneExpData中矩阵的列索引，提供每个基因的缩写（acronym）、Entrez ID、基因ID（gene_id）与基因名称（name）。
4. structInfo：用于标注Oh等人2014年发表于《自然》（Nature）的论文《小鼠脑介观连接组》（*A mesoscale connectome of the mouse brain*）所提及的213个脑结构的相关信息，原文刊于第508卷，第207页。每个结构配有其缩写、十六进制颜色码（color_hex_triplet）、结构ID、名称与分区标签（divisionLabel）。该表的每一行对应GeneExpData中矩阵的行索引。

请注意，本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。如需具体的引用规范，请在使用本数据集时参考艾伦研究所的引用政策（链接见下文）。

若你需要了解更多关于本数据集构建的细节，例如未经过Matlab处理的AllenSDK原始文件，或是关于如何通过AllenSDK获取数据并在Matlab中完成处理的更多信息，可随时联系我。后续我将在时间允许的情况下，将代码框架上传至GitHub。