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Nucleic Acids Res

BrainScope: interactive visual exploration of the spatial and temporal human brain transcriptome

Sjoerd M.H. Huisman, Baldur van Lew, Ahmed Mahfouz, Nicola Pezzotti, Thomas Höllt, Lieke Michielsen, Anna Vilanova, Marcel Reinders, and Boudewijn P. F. Lelieveldt

Gene t-SNE maps are robust and reproducible across donors. (A) The combined gene t-SNE map, showing previously reported stable gene modules (23). The map separates the 32 modules and shows their relationships. (B) The gene maps for each of the six donor brains. The maps are made using independent data sets, so they reflect the robustness of spatial gene expression patterns in the human brain. Data was pre-processed as in the original publication (23) to enable direct comparison of the WGCNA modules to the gene t-SNE maps.

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Spatial and temporal brain transcriptomics has recently emerged as an invaluable data source for molecular neuroscience. The complexity of such data poses considerable challenges for analysis and visualization. We present BrainScope: a web portal for fast, interactive visual exploration of the Allen Atlases of the adult and developing human brain transcriptome. Through a novel methodology to explore high-dimensional data (dual t-SNE), BrainScope enables the linked, all-in-one visualization of genes and samples across the whole brain and genome, and across developmental stages. We show that densities in t-SNE scatter plots of the spatial samples coincide with anatomical regions, and that densities in t-SNE scatter plots of the genes represent gene co-expression modules that are significantly enriched for biological functions. We also show that the topography of the gene t-SNE maps reflect brain region-specific gene functions, enabling hypothesis and data driven research. We demonstrate the discovery potential of BrainScope through three examples: (i) analysis of cell type specific gene sets, (ii) analysis of a set of stable gene co-expression modules across the adult human donors and (iii) analysis of the evolution of co-expression of oligodendrocyte specific genes over developmental stages. BrainScope is publicly accessible at www.brainscope.nl.

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Sjoerd M.H. Huisman, Baldur van Lew, Ahmed Mahfouz, Nicola Pezzotti, Thomas Höllt, Lieke Michielsen, Anna Vilanova, et al., BrainScope: interactive visual exploration of the spatial and temporal human brain transcriptome, Nucleic Acids Res, 45, p. e83, 2017.

BibTex 

@article{bib:huisman:2017,
    author       = { Huisman, Sjoerd M.H. and van Lew, Baldur and Mahfouz, Ahmed and Pezzotti, Nicola and Höllt, Thomas and Michielsen, Lieke and Vilanova, Anna and Reinders, Marcel and Lelieveldt, Boudewijn P. F. },    
    title        = { BrainScope: interactive visual exploration of the spatial and temporal human brain transcriptome },
    journal      = { Nucleic Acids Res },
    volume       = { 45 },
    year         = { 2017 },
    pages        = { e83 },
    doi          = { 10.1093/nar/gkx046 },
    pubmedid     = { 28132031 },
    url          = { https://publications.graphics.tudelft.nl/papers/249 },
}