Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Note: Coronal SectionDataSets span both hemispheres while sagittal SectionDataSets only span the left hemisphere. Voxels with no data are assigned a value of "-1".

Examples:

The expression data grid can be viewed in the Brain Explorer® 2 desktop program. Each grid voxel is rendered as a colorized sphere where the diameter represents expression energy and the color encodes expression intensity. In addition, a preview of the expression data grid is shown on the Web application as a series of maximum density projection images.

...

Figure: Screenshot of top returns of a correlation search for genes with similar expression as Neurod1 within the telencephalic telencephalic vesicle at age P4.

Example:

  • Correlation search for genes with similar expression to Neurod1 within Tel over multiple ages P4, P14,

    P28

    P28 

    No Format
    (http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_mouse_correlation
    \
    [row$eq17779
    \
    ]
    \
    
    [structures$eq'Tel'
    \
    ]
    \
    [ages$eq'P4','P14','P28'
    \
    ])

Figure: Screenshot of the top 2 returns (Sowaha, Prox1) of a correlation search for genes with similar expression as Neurod1 within the telencephalic vesicle at ages (left to right) P4, P14, P28.

Example:

  • Correlation search for genes with similar expression to Nr5a1 over the whole neural plate (NP) and across all 7 ages

    (

    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_mouse_correlation
    \
    [row$eq26171
    \
    ]
    \
    [structures$eq'NP'
    \
    ]
    )

Figure: Screenshot of the top returns of a correlation search for genes with similar expression as Nr5a1 over the whole neural plate (NP) and across all 7 ages. Each gene is represented by an expression "heatmap" for 11 gross regions.

...

*Note:* the structural hierarchy associated with the manual annotation differs from the Ontology used for informatics processing of the ISH data.

Examples:

  • Download manual annotation for gene Tcf7l2 at E11.5

    (

    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::ManualAnnotation,rma::criteria,
    \
    [section_data_set_id$eq100045897
    \
    ],
    rma::include,structure,rma::options
    \
    [order$eq'structures.graph_order$asc'
    \
    ]
    )
  • Search for E13.5 SectionDataSets with high intensity, regional expression in the diencephalon

    (

    No Format
    http://api.brain-map.org/api/v2/annotated_section_data_sets.xml?structures=112765096
    &intensity_values='High'&pattern_values='Regional'&age_names='E13.5'
    )
  • Download the structure ontology used for manual annotation

    No Format
    http://api.brain-map.org/api/v2/structure_graph_download/112755225.json

Figure: Screenshot of "Manual Annotation" example application showing the expression intensity, density and pattern attributes for level 5 structures for gene Tcf7l2 at E11.5 (id=100045897)