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Allen Brain Atlas API

The NIH Blueprint Non-Human Primate (NHP) Atlas consists of a suite of gene expression data, neuroanatomical data and informatics tools for exploring the cellular and molecular architecture of the developing postnatal rhesus macaque brain. Data includes:

Microdissection Microarray: Fine structure transcriptional profiling across postnatal development for fine nuclear subdivisions of the prefrontal cortex, primary visual cortex, hippocampus, amygdala and ventral striatum
Macrodissection Microarray: Gross structure transcriptional profiling across postnatal development for the same structures

From the API, you can:

Download expression values
Query the correlative and differential search services

Microdissection Microarray

Experimental Overview and Metadata

The NHP Developmental LMD Microarray Study is genome-wide microarray data profiling specific brain regions and fine nuclear subdivisions of these regions using rhesus macaque-specific DNA microarrays at four postnatal developmental stages.

Each sampling site is associated to a Structure by expert anatomist using cytoarchitectural information from multiple histological stains. Structures are arranged in a hierarchical organization. Each structure has one parent and denotes a "part-of" relationship. Structures are assigned a color to visually emphasize their hierarchical positions in the brain.

See the structure ontology page for more information.

Normalized microarray expression values can be downloaded in several ways:

From the web application Download page
From the connected data service in the API

All experimental data from this study is associated with the "Non-Human Primate LMD Microarray" Product. All probe and sampling site information can be accessed through the API using RMA queries.

Examples:

Downloading Expression Values

Normalized expression values can be obtained by specifying:

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

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

Example:

Download expression values for all 48 mo donors in structure "V1" for all probes associated with gene MET.

Find Donor ID for all 48 mo donors (id = 9878,11196,11272)

http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
rma::criteria,age[name$eq'48 mo'],organism[name$eq'Macaca mulatta'],
products[name$eq'Non-Human Primate LMD Microarray'],
rma::options[only$eq'donors.id']

Find Structure ID for "V1" (id = 10026)

http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
rma::criteria,[acronym$il'V1'],ontology[name$eq'Non-Human Primate Brain Atlas'],
rma::options[only$eq'structures.id']

Find AffymetrixMacaqueProbeset IDs associated with gene MET (id = 12414,29851,29853,29854,49439 )

http://api.brain-map.org/api/v2/data/query.xml?criteria=model::AffymetrixMacaqueProbeset,
rma::criteria,gene_association(gene[acronym$eq'MET']),
rma::options[only$eq'affymetrix_macaque_probesets.id'][order$eq'affymetrix_macaque_probesets.id']

Use Donor, Structure and AffymetrixMacaqueProbeset IDs as parameters to the connected service

http://api.brain-map.org/api/v2/data/query.json?criteria=
    service::nhp_lmd_microarray_expression[structures$eq10026]
      [probes$eq12414,29851,29853,29854,49439][donors$eq9878,11196,11272]

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

"probes":[
    {"id":12414,
    "name":"MmugDNA.19034.1.S1_at",
    "gene-id":183127,
    "gene-symbol":"MET",
    "gene-name":"met proto-oncogene (hepatocyte growth factor receptor)",
    "entrez-id":704562,"chromosome":"3","start-position":"n/a","end-position":"n/a",
    "expression_level":["4.3598","4.3794","4.3090","4.6997", ...]},
    {"id":29851,
    "name":"MmugDNA.34584.1.S1_at",
    "gene-id":183127,"gene-symbol":"MET",
    "gene-name":"met proto-oncogene (hepatocyte growth factor receptor)",
    "entrez-id":704562,"chromosome":"3","start-position":"n/a","end-position":"n/a",
    "expression_level":["4.2801","4.4093","4.1732","4.2536", ...]}, ...
    ],
"samples":[
    {"donor":{"id":11272,"name":"MMU36322","age":"48 mo","color":"333333"},
    "structure":{"id":10027,"name":"layer I of V1","abbreviation":"V1-1","color":"EDC9C0"},
    "top_level_structure":{"id":4004,"name":"occipital cortex","abbreviation":"Ocx","color":"E7ACA1"}},
    {"donor":{"id":11272,"name":"MMU36322","age":"48 mo","color":"333333"},
    "structure":{"id":10028,"name":"layer II of V1","abbreviation":"V1-2","color":"C73835"},
    "top_level_structure":{"id":4004,"name":"occipital cortex","abbreviation":"Ocx","color":"E7ACA1"}}, ...
    ]

Each probe contains information about:

the AffymetrixMacaqueProbeset (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).

Differential Search

Differential search find probes that show the greatest difference between two sets (target and contrast) of user-defined structures and donors. 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.

The differential search function can be access through the Web application or using the API.

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

Correlative Search

Correlative search finds probes with similar expression profile to the selected seed probe over all samples within a user-specified structure and for user-specified donors. Pearson's correlation coefficient is computed for all probes and results ranked in descending order.

This correlative search function can be access through the Web application or using the API.

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

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