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Download expression values for donor "H0351.1015" in structure "locus ceruleus" for all probes associated with gene SLC6A.

  • Find Donor ID for donor "H0351.1015" (id = 15496)
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,[name$eq'H0351.1015'], 
    rma::options[only$eq'donors.id']
    
  • Find Structure ID for structure "locus ceruleus" (id = 9148)
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'locus ceruleus'],ontology[name$eq'Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Find probes Probes associated with gene SLC6A (id = 1023146,1023147 )
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Probe,
    rma::criteria,[probe_type$eq'DNA'],products[abbreviation$eq'HumanMA'],gene[acronym$eq'SLC6A2'],
    rma::options[only$eq'probes.id']
    
  • Use donorDonor, structure Structure and probe Probe IDs as parameters to the connected service
    Code Block
    http://api.brain-map.org/api/v2/data/query.json?criteria=
        service::human_microarray_expression[probes$eq1023146,1023147][donors$eq15496][structures$eq9148] 
    

The output of the service is two top level ordered arrays "probes" and "samples". For example:

Code Block
"probes":[{
    "id":1023146,
    "name":"A_23_P358345",
    "gene-id":6494,
    "gene-symbol":"SLC6A2",
    "gene-name":"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2",
    "entrez-id":6530,"chromosome":"16","start-position":"n/a","end-position":"n/a",
    "expression_level":["13.2802","13.9603","13.9650"],
    "z-score":["9.3381","9.8663","9.8700"]},
    {
    "id":1023147,
    "name":"CUST_16472_PI416261804",
    "gene-id":6494,
    "gene-symbol":"SLC6A2",
    "gene-name":"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2",
    "entrez-id":6530,"chromosome":"16","start-position":"n/a","end-position":"n/a",
    "expression_level":["8.1878","8.5644","8.2310"],
    "z-score":["9.3201","9.8326","9.3790"]}
    ],
"samples":[
    {"donor":{"id":15496,"name":"H0351.1015","age":"49 years","color":"C2C200"},
    "sample":
        {"well":148955246,"polygon":127107914,"mri":[95,121,126]},
        "structure":{"id":9149,"name":"locus ceruleus, Left","abbreviation":"LC","color":"00FFAA"},
        "top_level_structure":{"id":9135,"name":"Pontine Tegmentum","abbreviation":"PTg","color":"00FFAA"}},
    {"donor":{"id":15496,"name":"H0351.1015","age":"49 years","color":"C2C200"},
    "sample":
        {"well":148955204,"polygon":126786164,"mri":[97,151,131]},
        "structure":{"id":9149,"name":"locus ceruleus, Left","abbreviation":"LC","color":"00FFAA"},
        "top_level_structure":{"id":9135,"name":"Pontine Tegmentum","abbreviation":"PTg","color":"00FFAA"}},    
    {"donor":{"id":15496,"name":"H0351.1015","age":"49 years","color":"C2C200"},
    "sample":
        {"well":156435966,"polygon":126789834,"mri":[96,159,134]},
        "structure":{"id":9149,"name":"locus ceruleus, Left","abbreviation":"LC","color":"00FFAA"},
        "top_level_structure":{"id":9135,"name":"Pontine Tegmentum","abbreviation":"PTg","color":"00FFAA"}}
    ]

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Usage of this service is demonstrated in the scatter plot and SPM example applications. Also see example code on how to transform each microarray sample to MNI space.

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.

This Image Added The differential  search function can be access through the Web application or using the RMA Services and Pipesthe API.

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

Example:
Differential search for genes with higher expression in thalamus than the cerebral cortex

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  • 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'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$il'cerebral cortex'],ontology[name$eq'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_
    differentialto perform the differential search
    differential[structures1$eq4008][structures2$eq4392]
    
  • Visualize the same search result in the Web application

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Usage of this service is demonstrated in the SPM example application.http://iwarehouse/doc/index.html

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.

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