Versions Compared

Key

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

...

Download RNA-Seq expression values for samples from donor "H376.VI.52" associated with gene CARTPT

  • Find Donor ID for "H376.VI.52" (id = 12890)
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,[name$eq'H376.VI.52'],
    rma::options[only$eq'donors.id']
    
  • Find Gene ID associated with gene CARTPT (id = 1098278)
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Gene,
    rma::criteria,[ensembl_id$nenil][acronym$eq'CARTPT'],organism[name$eq'Homo Sapiens'],
    rma::options[only$eq'genes.id']
    
  • Use set = rna_seq_genes, Gene ("probe") and Donor IDs as parameter to the service::dev_human_expression
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.json?criteria=service::dev_human_expression
        [set$eq'rna_seq_genes'][probes$eq1098278][donors$eq12890]
    

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

Code Block

"probes":[
    {"id":1098278,
    "name":"ENSG00000164326",
    "gene-id":9463,
    "gene-symbol":"CARTPT","gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":"n/a","end-position":"n/a",
    "expression_level":["6.1242","5.3674","6.2563",...]}
    ],
"samples":[
    {"donor":{"id":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "structure":{"id":10173,"name":"dorsolateral prefrontal cortex","abbreviation":"DFC","color":"D4B235"},
     "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}},
     {"donor":{"id":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "structure":{"id":10185,"name":"ventrolateral prefrontal cortex","abbreviation":"VFC","color":"C2A335"},
     "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}},
     {"donor":{"id":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "structure":{"id":10278,"name":"anterior (rostral) cingulate (medial prefrontal) cortex","abbreviation":"MFC","color":"E26880"},
     "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}}, ...
     ],

Each probe (Gene) contains information about:

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

Each sample contains information about:

  • 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).

Example:

Download RNA-Seq expression values for samples from donor "H376.VI.52" and all exons associated with gene CARTPT

...