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  • the Donor (id, name, age),
  • the associated Structure (id, name, acronym and color), and
  • the associated top (coarse) level Structure (id, name, acronym and color).

Differential Search

Differential search find 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 less than the average expression level of samples in the target 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.

The differential  search function can be access through the Web application or using the API.

See the connected service page for definitions of service::dev_human_microarray_differential parameters.

Example:
Differential search for genes with higher expression in "thalamus" than the "transient structures of forebrain"

  • Find Structure ID for "thalamus" (id = 4392)
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'thalamus'],ontology[name$eq'Developing Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Find Structure ID for "cerebral cortex" (id = 4008)
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'transient structures of forebrain'],ontology[name$eq'Developing Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Use Structure IDs as parameters to the connected service
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::human_microarray_differential
        [structures1$eq4008][structures2$eq4392][sort_by$eq'fold-change']
    
  • Visualize the same search result in the Web application¬†

Image Added

Figure: Screenshot of top returns of a differential search for genes with higher expression in the thalamus than the cerebral cortex. Z-score heatmap shows enrichment (red) in the thalamus (structure color: light green) compare to other brain regions.

Correlative Search