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Normalized expression values can be obtained by specifying:

  • a list of probes

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  • a list of donors (optional), and
  • a list of structures (optional)

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

Example:

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

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gene SLC6A.

  • Find 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 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 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 donor, structure and probe IDs as parameters to the connected service
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.json?criteria=
        service::human_microarray_
    expressionto download expression values
    expression[probes$eq1023146,1023147][donors$eq15496][structures$eq9148] 
    

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

Code Block
"samples":[
    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":986115496,"name":"H0351.20011015","age":"2449 years","color":"EC891DC2C200"},
    "sample":
        "sample":{"well":154148955246,"polygon":27255127107914,"mri":[7495,96121,29126]},
        "structure":{"id":40559149,"name":"anteriorlocus orbital gyrusceruleus, RightLeft","abbreviation":"AOrGLC","color":"E8BF5900FFAA"},
        "top_level_structure":{"id":40099135,"name":"FrontalPontine LobeTegmentum","abbreviation":"FLPTg","color":"E8CD5900FFAA"}},
       {"donor":{"id":986115496,"name":"H0351.20011015","age":"2449 years","color":"EC891DC2C200"},
    "sample":
    "sample":    {"well":442148955204,"polygon":28152126786164,"mri":[13797,89151,57131]},
        "structure":{"id":40799149,"name":"frontallocus operculumceruleus, Left","abbreviation":"froLC","color":"E8C15900FFAA"},
        "top_level_structure":{"id":40099135,"name":"FrontalPontine LobeTegmentum","abbreviation":"FLPTg","color":"E8CD5900FFAA"}},
       ...
       ]

"probes":[
    {"donor":{"id":1053219,
     15496,"name":"CUST_645_PI417557136H0351.1015",
     "gene-id":5141,
     "gene-symbol":"PDYN""age":"49 years","color":"C2C200"},
     "gene-namesample":"prodynorphin",
     "entrez-id":5173,
     "expression_level":[6.01268,3.15029,4.33954,3.7882,3.37497,3.67553,5.15228,3.54207,2.54943,3.26123,2.81641, ...   {"well":156435966,"polygon":126789834,"mri":[96,159,134]},
        "structure":{"id":1053228,
     "name":"CUST_636_PI417557136",
     "gene-id":5141,
9149,"name":"locus ceruleus, Left","abbreviation":"LC","color":"00FFAA"},
        "gene-symboltop_level_structure":{"PDYNid",
     "gene-:9135,"name":"prodynorphinPontine Tegmentum",
     "entrez-id":5173,"abbreviation":"PTg","color":"00FFAA"}}
     "expression_level":[7.04102,5.27998,4.7581,4.57514,5.80835,4.90257,6.41983,5.70795,5.06719,3.63895,3.86425, ...]},
    ...
    ]
]

Each probe contains information about:

  • the Probe(id, name), and
  • the Gene (id, acronym, name, entrez-id), along with
  • a vector of normalized expression values in the same order as the "samples" array.
  • a vector of z-score values in the same order as the "samples" array. Note: z-score is computed independently for each probe over all donors and samples.

Each sample contains information about:

  • the Donor (id, name, age),
  • the Sample (well id and (x,y,z) coordinate in the MR volume in millimeters),
  • the associated Structure (id, name, acronym and color), and
  • the associated top (coarse) level Structure (id, name, acronym and color).

Each probe contains information about:

  • the Probe(id, name), and
  • the Gene (id, acronym, name, entrez-id), along witha vector of normalized expression values in the same order as the "samples" array.

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.http://iwarehouse/doc/index.html

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.

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