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ALLEN BRAIN ATLAS API
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 were also registered to MNI space to enable cross-individual comparisons.
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Download expression values
Query the correlative and differential search services
Download MRI images
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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, sets of tiling probes were designed.
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- All donors in the Product
- All sampling sites in the Product
- All microarray probes in the Product
- All microarray probes associated with gene prodynorhphin (PDYN)
- All samples associated with donor "H0351.2001" and the dentate gyrus
- Download an "raw" Aglient output file for one sample using the download-link (warning: large file)
Supplemental RNA-Sequencing Data
RNA-Sequencing (RNA-Seq) data were generated for a selected set of 240 samples (120 from each brain) representing matched cortical and sub-cortical regions across two brains (H0351.2001 and H0351.2002). The gene expression data (both raw and TPM counts) can be downloaded from the web application Download page.
Through a quantitative comparison of microarray and RNA-Seq data, a set of quality control metrics has been computed for each Agilent microarray probe which allows a user to filter out problematic probes or choose the most reliable probe for each gene. The probe metric table and metadata can be downloaded here.
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DOWNLOADING EXPRESSION VALUES
Normalized expression values can be obtained by specifying:
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Usage of this service is demonstrated in the scatter plot and SPM example applications. Also see example code on how to transform each microarray sample to MNI space.
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DIFFERENTIAL SEARCH
The differential search function finds probes that show the greatest difference between two sets (target and contrast) of user-defined structures. For each probe, a 2-sample t-test is performed followed by Benjamini and Hochberg false discovery rate correction. The null hypothesis is that the average expression level of samples in the contrast set of structures is greater than or equal to the average expression level of samples in the target set of structures. A statistically significant result (p-value less than user-defined threshold) allows us to reject the null hypothesis and conclude that the average expression level of samples in the target set of structures is greater than the average expression level of samples in the contrast set of structures. Resulting p-values are sorted in ascending order. Search results can also be sorted by fold-change (log ratio of expression) in descending order.
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Usage of this service is demonstrated in the SPM example application.
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CORRELATIVE SEARCH
The correlative search function finds probes with expression profile similar to that of a selected seed probe over all samples within a user-specified structure. Pearson's correlation coefficient is computed for all probes and the results ranked in descending order.
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Figure: Screenshot of top returns of a correlative search for probes with similar expression to a PVALB probe with expression values displayed as a z-score heatmap.
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MAGNETIC RESONANCE IMAGING
T1-weighted MPRAGE scans were acquired for the postmortem brains using 3T Siemens Trio MR scanners (TI=900ms, TR=1900ms, TE=3.03ms, 9 degree flip angle, 1mm isotropic voxels). Scans were performed in cranio for some brains and ex cranio for others. See the Microarray whitepapers for more specific scan sequence details for each brain.
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