ArticleNucleic acids research2017
BrainScope: interactive visual exploration of the spatial and temporal human brain transcriptome.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Review
- Functional genomic imaging (FGI), a virtual tool for visualization of functional gene expression modules in heterogeneous tumor samples.Biology direct · 2025Article
- Spatiotemporal expression patterns of genes coding for plasmalemmal chloride transporters and channels in neurological diseases.Molecular brain · 2023Article
- SpatialCorr identifies gene sets with spatially varying correlation structure.Cell reports methods · 2022Article
- Collective genomic segments with differential pleiotropic patterns between cognitive dimensions and psychopathology.Nature communications · 2022Article
- Identifying multicellular spatiotemporal organization of cells with SpaceFlow.Nature communications · 2022Article
- Temporal modelling using single-cell transcriptomics.Nature reviews. Genetics · 2022Review
- Timing and localization of myasthenia gravis-related gene expression.The European journal of neuroscience · 2021Review
- Molecular characterization of the stress network in individuals at risk for schizophrenia.Neurobiology of stress · 2021Article
- Exploring the secrets of brain transcriptional regulation: developing methodologies, recent significant findings, and perspectives.Brain structure & function · 2021Review
- Identification of Cysteine Protease Inhibitor CST2 as a Potential Biomarker for Colorectal Cancer.Journal of Cancer · 2021Article
- Cellular resolution in clinical MALDI mass spectrometry imaging: the latest advancements and current challenges.Clinical chemistry and laboratory medicine · 2020Review
- Visualizing and Interpreting Single-Cell Gene Expression Datasets with Similarity Weighted Nonnegative Embedding.Cell systems · 2018Article
- Analyzing the similarity of samples and genes by MG-PCC algorithm, t-SNE-SS and t-SNE-SG maps.BMC bioinformatics · 2018Article
- A structural equation model for imaging genetics using spatial transcriptomics.Brain informatics · 2018Article
- Interactive Visual Exploration of 3D Mass Spectrometry Imaging Data Using Hierarchical Stochastic Neighbor Embedding Reveals Spatiomolecular Structures at Full Data Resolution.Journal of proteome research · 2018Article
- Natriuretic Peptides in Post-mortem Brain Tissue and Cerebrospinal Fluid of Non-demented Humans and Alzheimer's Disease Patients.Frontiers in neuroscience · 2018Article
- Co-expression Patterns betweenFrontiers in molecular neuroscience · 2017Article
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9 authors.
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Abstract
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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