A FreeSurfer view of the cortical transcriptome generated from the Allen Human Brain Atlas

The Allen Human Brain Atlas provides an anatomically detailed view of gene expression in the brain. This full transcriptomic dataset contains over 200 million expression values. To facilitate use of this resource, we distilled the data into a matrix of 20,737 genes by 68 cortical regions that represent the automatically segmented FreeSurfer regions (Desikan-Killiany parcellation). In this data report, we describe the Allen-FreeSurfer mapping, sampling information and provide regional values of gene expression. The resulting cortical transcriptome facilitates interpretation of human neuroimaging findings by providing a molecular context. Read the full data report at: http://journal.frontiersin.org/article/10.3389/fnins.2015.00323/full AllenHBA_to_DKRegion_Map.xls - Excel file containing the mapping from Allen Brain Atlas samples to the FreeSurfer cortical regions. Each sample is referenced with a unique identifier by combining the donor ID with the x, y and z MNI152 coordinates (“10021_5.1_27.1_28.6“ for example). DKRegionStatistics.tsv - Tab separated file characterizing the FreeSurfer cortical regions. This file lists how many donors contribute to each region, Allen Brain Atlas samples per region and alternative identifiers. AllenHBA_DK_ExpessionMatrix.tsv - tab separated file containing correlation to the median values across the donors (left hemisphere only, column named ”Average donor correlation to median”) and gene expression values across the 68 FreeSurfer cortical regions (columns). This file can be opened with read.table in R or as a tab separated file in a spreadsheet program. ConsistentGOGroups.tsv – Gene Ontology enrichment analyses results for the consistency measure. InconsistentGOGroups.tsv – Gene Ontology enrichment analyses results for the consistency measure (with high ranked groups showing more inconsistency). CreateExpressionLUT.r - This R script provides the method to load and convert expression values for a specific gene into a color lookup table that can be used to visualize the averaged expression values in FreeSurfer. CreateColorBar.r - This R script will create a color bar to complement the TKSurfer generated images.

艾伦人脑图谱（Allen Human Brain Atlas）提供了大脑基因表达的解剖学细节视图。该完整转录组数据集包含超过2亿个基因表达量数值。为便于该资源的应用，我们将原始数据精简为一个包含20737个基因与68个皮层区域的矩阵，这些皮层区域对应自动分割的FreeSurfer脑区划分（Desikan-Killiany parcellation）。
在本数据报告中，我们详细阐述了艾伦-FreeSurfer映射规则、采样相关信息，并提供了各区域的基因表达量数值。最终生成的皮层转录组可为人类神经影像学研究结果的解读提供分子层面的背景支撑，助力相关科学发现的阐释。完整数据报告可通过以下链接查阅：http://journal.frontiersin.org/article/10.3389/fnins.2015.00323/full

- AllenHBA_to_DKRegion_Map.xls：该Excel文件收录了艾伦脑图谱采样点与FreeSurfer皮层区域的映射关系。每个采样点通过将供体ID与x、y、z轴的MNI152坐标相结合生成唯一标识符（例如“10021_5.1_27.1_28.6”）。
- DKRegionStatistics.tsv：该制表符分隔文件用于表征FreeSurfer皮层区域，其中列出了每个区域对应的供体数量、该区域内的艾伦脑图谱采样点数量以及替代标识符。
- AllenHBA_DK_ExpessionMatrix.tsv：该制表符分隔文件包含了与各供体（仅左半球）中位数表达量的相关性数据（列名为“与中位数的平均供体相关性”），以及68个FreeSurfer皮层区域（以列形式呈现各区域）的基因表达量数值。该文件可通过R语言的read.table函数读取，或在电子表格软件中以制表符分隔文件格式打开。
- ConsistentGOGroups.tsv：针对一致性度量的基因本体（Gene Ontology, GO）富集分析结果文件。
- InconsistentGOGroups.tsv：针对一致性度量的基因本体富集分析结果文件（排名靠前的分组体现出更高的不一致性）。
- CreateExpressionLUT.r：该R脚本提供了将特定基因的表达量值加载并转换为颜色查找表的方法，可用于可视化FreeSurfer中的平均表达量值。
- CreateColorBar.r：该R脚本可生成用于配套TKSurfer生成图像的色条。