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Figure: Screenshot of top returns of a differential search for genes with higher expression in the thalamus than the transient structures of forebrain. Z-score heatmap shows enrichment in the thalamus compare to other brain regions.

Correlative Search

Correlative search finds probes with similar expression profile to the selected seed probe over all samples within a user-specified structure. Pearson's correlation coefficient is computed for all probes and results ranked in descending order.

This correlative 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_correlation parameters.

Example:
Correlative search for probes with similar expression to PVALB probe CUST_11451_PI416261804 over the whole neural plate

  • Find Probe ID for probe "CUST_11451_PI416261804" (id = 1052410)
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Probe,
    rma::criteria,[name$eq'CUST_11451_PI416261804'],
    rma::options[only$eq'probes.id']
    
  • Find Structure ID for "neural plate" (id = 10153)
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'neural plate'],ontology[name$eq'Developing Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Use Probe and Structure IDs as parameters to the connected service
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_microarray_correlation
        [probes$eq1052410][structures$eq10153]
    
  • Visualize the same search result in the Web application

Image Added

Figure: Screenshot of top returns of a correlative search for probes with similar expression to a PVALB probe with expression values displayed as a z-score heatmap.