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The Allen Human Brain Atlas is a multimodal atlas of the human brain that integrates anatomic and microarray-based gene expression information. Microarray sampling sites (~400-1000 sites per brain) were identified by expert anatomists using cytoarchitectural information from multiple histological stains. Sampling site delineations in the high resolution histological images were subsequently mapped into each individual's MR image space to provide 3-D anatomical context. All brains are also registered to MNI space to enable cross-individual comparisons.

From the API, you can:


Image Added Download expression values
Image Added Query the correlative and differential search services
Image Added Download MRI images

Experimental Overview and Metadata

RNA isolated from each sample area was hybridized to a custom Agilent 8x60k microarray chip to measure gene expression over the transcriptome. All least two different probes were available for 93% of genes. Probes were located on different exons as much as possible when multiple probes were available for a gene. For 60 genes, a set of tiling probes were probes was designed.

Each sampling site is associated to a Structure by expert anatomist using cytoarchitectural information from multiple histological stains. Structures are arranged in a hierarchical organization. Each structure has one parent and denotes a "part-of" relationship. Structures are assigned a color to visually emphasize their hierarchical positions in the brain.

See the structure ontology page for more information.

Gene expression data for samples passing quality control were normalized first within a single brain using a cross-batch normalization algorithm called ComBat. In order to allow comparison across two or more brains, a cross-brain normalization was performed by aligning the mean 75th percentile expression values of all internal reference control samples of each brain to that of the first brain (H0351.2001). are normalized to enable cross-comparison between batches and donors.  See the whitepaper for more details on microarray data generation and processing.

Image Added Normalized microarray expression values can be downloaded in a simple numerical matrix format from the web application or through the Microarray Data Service.