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  • 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]
    

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  • Use set = rna_seq_exons, GoExon ("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$eq'rna_seq_exons'][probes$eq1062744,1062745,1062746][donors$eq12890]
    

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  • Use set = exon_microarray_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$eq'exon_microarray_genes'][probes$eq9463][donors$eq12296]
    

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  • Use set = exon_microarray_exons, AffymetrixProbeset ("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$eq'exon_microarray_exons'][probes$eq547104,547105,547106,547107,547108][donors$eq12296]
    

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  • 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 (set = rna_seq_genes)
    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']
    
  • Differential search for exon-level RNA-Seq data (set = rna_seq_exons )
    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 (set = exon_microarray_genes )
    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 (set = exon_microarray_exons )
    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']
    
  • Visualize the gene-level RNA-Seq differential search result in the Web application

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  • 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']
    
  • Find Donor IDs for donors within age 8-9 pcw (id = 12833,13058)
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,products[name$eq'Developing Human Transcriptome'],age[embryonic$eqtrue][days$ge56][days$le63],
    rma::options[only$eq'donors.id']
    
  • Find Donor IDs for donors within age 10-12 pcw (id = 12835,12960,13060)
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,products[name$eq'Developing Human Transcriptome'],age[embryonic$eqtrue][days$ge56][days$le63],
    rma::options[only$eq'donors.id']
    
  • Differential search for gene-level RNA-Seq data (set = rna_seq_genes)
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
        [set$eq'rna_seq_genes'][donors1$eq12835,12960,13060][donors2$eq12833,13058]
        [structures1$eq10153][structures2$eq10153][sort_by$eq'fold-change']
    
  • Differential search for exon-level RNA-Seq data (set = rna_seq_exons )
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
        [set$eq'rna_seq_exons'][donors1$eq12835,12960,13060][donors2$eq12833,13058]
        [structures1$eq10153][structures2$eq10153][sort_by$eq'fold-change']
    
  • Differential search for gene-level exon microarray data (set = exon_microarray_genes )
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
        [set$eq'exon_microarray_genes'][donors1$eq12835,12960,13060][donors2$eq12833,13058]
        [structures1$eq10153][structures2$eq10153][sort_by$eq'fold-change']
    
  • Differential search for probeset-level exon microarray data (set = exon_microarray_exons )
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
        [set$eq'exon_microarray_exons'][donors1$eq12835,12960,13060][donors2$eq12833,13058]
        [structures1$eq10153][structures2$eq10153][sort_by$eq'fold-change']
    

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  • Correlative search for gene-level RNA-Seq data  ( seed Ensembl Gene id = 1089164, set = rna_seq_genes )
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
        service::dev_human_correlation[set$eqrna_seq_genes][probes$eq1089164][structures$eq10153]
    
  • Correlative search for exon-level RNA-Seq data  ( seed GoExon id = 949465, set = rna_seq_exons )
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
        service::dev_human_correlation[set$eqrna_seq_exons][probes$eq949465][structures$eq10153]
    
  • Correlative search for gene-level exon microarray data (seed NCBI Gene id = 5784, set = exon_microarray_genes )
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
        service::dev_human_correlation[set$eqexon_microarray_genes][probes$eq5784][structures$eq10153]
    
  • Correlative search for probeset-level exon microarray data ( seed AffymetrixProbeset id = 704598, set = exon_microarray_exons )
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
        service::dev_human_correlation[set$eqexon_microarray_exons][probes$eq704598][structures$eq10153]
    

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  • Find Donor ID for "H376.IIIA.02" (id = 12840)
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,[name$eq'H376.IIIA.02'],
    rma::options[only$eq'donors.id']
    
  • Find Structure ID for "cerebellar cortex" (id = 10657)
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'cerebellar cortex'],ontology[name$eq'Developing Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Find Probes associated with gene SLC6A2(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::dev_human_microarray_expression[probes$eq1023146,1023147][donors$eq12840][structures$eq10657]
    

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  • Find Structure ID for "thalamus" (id = 10390)
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'thalamus'],ontology[name$eq'Developing Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Find Structure ID for "transient structures of forebrain" (id = 10506)
    Code Block
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'transient structures of forebrain'],ontology[name$eq'Developing 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::dev_human_microarray_differential
        [structures1$eq10506][structures2$eq10390][sort_by$eq'fold-change']
    
  • Visualize the same search result in the Web application 

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  • 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

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