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Code Block
"probes":[
    {"id":547104,
    "name":"ENSG00000164326",
    "gene-id":9463,
    "gene-symbol":"CARTPT",
    "gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":71015057,"end-position":71015120,
    "expression_level":["3.8656","3.4666","4.1867", ... ],
    "z-score":["0.0678","-1.0078","0.9335", ... ]},
    {"id":547105,
    "name":"ENSG00000164326",
    "gene-id":9463,
    "gene-symbol":"CARTPT",
    "gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":71015125,"end-position":71015265,
    "expression_level":["8.4237","8.9389","8.1073", ... ],
    "z-score":["1.7676","2.2219","1.4887","1.5533", ... ]}, ...
    ],
"samples":[
    {"donor":{"id":12296,"name":"H376.VI.50","age":"4 mos","color":"80FF80"},
    "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":12296,"name":"H376.VI.50","age":"4 mos","color":"80FF80"},
    "structure":{"id":10185,"name":"ventrolateral prefrontal cortex","abbreviation":"VFC","color":"C2A335"},
    "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}}, ...
    ]

Each probe (Gene) contains information about:

  • the AffymetrixProbeset (id), 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, and
  • a vector of z-score values in the same order as the "samples" array. Note: z-score is computed independently over all samples for each gene.

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).

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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|http://www.brainspan.org/rnaseq/searches?domain1=10173,10185,10278,10194,10163,10291,10208,10209,10225,10236,10235,10243,10252,10268,10269,10294,10361,10551,10550,10552,10333,10391,10398,10665,10656,10657&domain2=10333&stage1=IIA,IIB,IIIA,IIIB,IV,V,VI,VII,VIII,IX,X,XI&stage2=IIA,IIB,IIIA,IIIB,IV,V,VI,VII,VIII,IX,X,XI&search_type=differential]

Each probe (Gene) contains information about:

  • the AffymetrixProbeset (id), 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, and
  • a vector of z-score values in the same order as the "samples" array. Note: z-score is computed independently over all samples for each gene.

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).

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.

Image Added 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_differential parameters.

Example:

Differential search for genes with higher expression in "striatum" than the whole "neural plate" over all donors for each of the four types of expression data.

  • Find Structure ID for "striatum" (id = 10333 )
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'striatum'],ontology[name$eq'Developing Human Brain Atlas'],
    rma::options[only$eq'structures.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']
    
  • Differential search for gene-level RNA-Seq data
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
        [set$eq'rna_seq_genes'][structures1$eq10153][structures2$eq10333][sort_by$eq'fold-change']
    
  • Visualize the search result in the Web application
  • Differential search for exon-level RNA-Seq data
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
        [set$eq'rna_seq_exons'][structures1$eq10153][structures2$eq10333][sort_by$eq'fold-change']
    
  • Differential search for gene-level exon microarray data
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
        [set$eq'exon_microarray_genes'][structures1$eq10153][structures2$eq10333][sort_by$eq'fold-change']
    
  • Differential search for probeset-level exon microarray data
    Code Block
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
        [set$eq'exon_microarray_exons'][structures1$eq10153][structures2$eq10333][sort_by$eq'fold-change']
    

Correlative Search

Prenatal LMD Microarray

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