brainscope.app Open in urlscan Pro
80.69.67.17  Public Scan

Form analysis
0 forms found in the DOM

Text Content

Toggle navigation BrainScope
 * Anonymous

 * FAQ
 * Show tutorial
 * Enable tooltips
 * Help
   
   First load a data set
   
   Then do one of the following:
   
    * Hover over the maps to explore the data
    * Load predefined selections
    * Use "Upload selections" to add your own selections
    * Right-click on a map for extra options:
      * Change the selection mode
      * Set the number of neighbouring points for selections
      * Enable the density view on a map
      * Export the maps as images
    * Right-click on a loaded selection for GO term analysis or to export gene
      or sample lists
   
   Browser compatibility

   
 * Acknowledgements
   
   
      BRAINSCOPE
   
      WHEN USING THE BRAINSCOPE PORTAL IN YOUR PUBLICATIONS, PLEASE CITE THE
      FOLLOWING PAPER:
       * HUISMAN, S. M. H., VAN LEW, B., MAHFOUZ, A., PEZZOTTI, N., HöLLT, T.,
         MICHIELSEN, L., VILANOVA, A., REINDERS, M.J.T., LELIEVELDT, B. P. F.
         (2017)
       * BRAINSCOPE: INTERACTIVE VISUAL EXPLORATION OF THE SPATIAL AND TEMPORAL
         HUMAN BRAIN TRANSCRIPTOME. NUCLEIC ACIDS RESEARCH.
       * WEBSITE: DOI:10.1093/NAR/GKX046
   
    * DATA AND IMAGES USED ON THIS WEBSITE ARE DERIVED FROM THE ONLINE RESOURCES
      OF THE ALLEN INSTITUTE FOR BRAIN SCIENCE AND THE ALLEN BRAIN ATLAS © 2015
      ALLEN INSTITUTE FOR BRAIN SCIENCE.
      PLEASE ADHERE TO THE ALLEN INSTITUTE CITATION POLICY.
      
      PUBLICATIONS AND WEBSITE CITATIONS:
      
      1. * Allen Human Brain Atlas
         * Primary publication: Hawrylycz, M.J. et al. (2012) An anatomically
           comprehensive atlas of the adult human transcriptome, Nature 489:
           391-399. doi: 10.1038/nature11405
         * Website: Allen Human Brain Atlas © 2015 Allen Institute for Brain
           Science.
           
      2. * BrainSpan Atlas of the Developing Human Brain
         * Primary publication: Miller, J.A. et al. (2014) Transcriptional
           landscape of the prenatal human brain, Nature 508: 199-206.
           doi:10.1038/nature13185
         * Website: BrainSpan Atlas of the Developing Human Brain © 2015 Allen
           Institute for Brain Science.
           
      3. * Selection stable modules
         * Primary publication: Hawrylycz, M. J., Miller, J. A., Menon, V.,
           Feng, D., Dolbeare, T., Guillozet-Bongaarts, A. L., … Lein, E.
           (2015). Canonical genetic signatures of the adult human brain. Nature
           Neuroscience, 18(12), 18321844
         * Website: doi:10.1038/nn.4171
           
      4. * Selection cell types
         * Primary publication: Zhang, Y., Chen, K., Sloan, S. a, Bennett, M.
           L., Scholze, A. R., Keeffe, S. O., … Wu, X. J. Q. (2014). An
           RNA-Sequencing Transcriptome and Splicing Database of Glia , Neurons
           , and Vascular Cells of the Cerebral Cortex. The Journal of
           Neuroscience, 34(36), 119
         * Website: doi:10.1523/JNEUROSCI.1860-14.2014
           
   
    * 
      License information for libraries used in Brainscope
      
   
    * Collaborating institutions:
      * TUDelft LUMC STW
    * Project funding: This research has received partial funding from the Dutch
      Technology Foundation STW, as part of the STW project 12721: “Genes in
      Space" and 12720: “VANPIRE", under the IMAGENE STW Perspective program.
    * External GO-Term Analysis provided by
      1. Enrichr
      2. ToppGene
      3. g:Profiler
         Please observe the terms of use of these services.

Change the map settings

 * Selection method
   
   Select points by mouse-over, by drawing around them, or based on a property
   value.
   
   In mouse-over mode, clicking adds the selection to the list of loaded
   selections. For property based selection, use the button.

 * Nearest neighbours
   
   For mouse-over and property based selection, the seed point of the selection
   can be included or excluded (to only select neighbours).

 * Density plot
   
   Activate the density plot. This reveals densely clustered regions in the map.

 * Plot to image
   
   Save the current plot or all plots as png files.

The thematic map

 * View brain regions
   
   The thematic map will show gene expression for selected genes, and is
   coloured according to the Allen Reference Atlas.

 * Add brain slices (if applicable)
   
   Scroll down to select brain slices to view.

Additional images for the thematic map

Using the scatter plots:

 * Mouse over
   
   Mouse over to see information on individual points.

 * Zoom to cursor
   
   When the cursor is positioned over a map, the scroll wheel (or two-finger
   swipe on some OSes) may be used to zoom

 * Selection settings
   
   Right-click to reveal advanced selection options (selection mode,
   neighbouring points, density map and image export).

Data/Predefined selections/Ontology

 * Data Sets:
   
   Select a data set for viewing. It will load the maps defined in the datasets.

 * Predefined selections:
   
   In some cases predefined selection sets may appear. Select one to add it to
   the list of loaded selections.

 * Navigate ontology:
   
   When relevant, an ontology of brain regions is displayed, which can be used
   for selection.

Loaded selections

 * View selections
   
   This shows a list of all selections (genes or samples) with their
   descriptions and colours. The colour of a gene set selection can be changed
   by clicking on the colour picker.

 * Analyse selections
   
   Right-click on a selection for editing, gene ontology analysis and exporting.

 * Remove selections
   
   Use the buttons at the bottom to deselect all or remove selections from the
   list.

Upload selections

 * Selection from CSV file
   
   Upload a CSV file with identifiers.

 * Selection based on a property value
   
   Enter comma, semicolon or newline separated ids, and select the correct
   identifier in the property field.


PLEASE LOAD A DATA SET...






< Back to BrainScope
 
Data sets
Predefined selections
 

Adult human (dual explorer)



Adult human (comparative explorer)



Developing human (comparative explorer)










Loaded selections
Selection
Group
Description
Color picker








Clear/delete
Deselect
Delete last
Delete all

Upload selections