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 rhesus macaque brain. Data includes:

From the API, you can:

Download expression values
Query the correlative and differential search services

Microdissection Microarray

Experimental Overview and Metadata

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

Each sampling site was associated to a Structure by expert anatomists using cytoarchitectural information from multiple histological stains. Structures are organized hierarchically into a tree in which children structures are “parts of” their parent structure. Structures are assigned colors that visually emphasize the hierarchical relationships.

See the structure ontology page for more information.

Normalized microarray expression values can be downloaded in several ways:

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:

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 "V1-1" for all probes associated with gene MET.

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","4.4762","4.4883"],
    "z-score":["-0.3668","0.2633","0.3287"]},
    {"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","4.1808","4.0958"],
    "z-score":["0.0110","-0.2272","-0.4310"]}, ...
    ],
"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":11196,"name":"MMU36358","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":9878,"name":"MMU36468","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"}}
]

Each probe contains information about:

Each sample contains information about:

Differential Search

The differential search function finds 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 greater than or equal to the average expression level of samples in the target set of structures. A statistically significant result (p-value less than user-defined threshold) allows us to reject the null hypothesis and conclude that the average expression level of samples in the target set of structures is greater than the average expression level of samples in the contrast 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 accessed through the Web application or using the API.

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

Example:
Differential search for genes with higher expression in "basal ganglia" than in the "neocortex"

Figure: Screenshot of top returns of a differential search for genes with higher expression in the basal ganglia than
in the neocortex represented as a z-score heatmap ranging from green (below mean) to red (above mean).

Example:
Differential search for genes with higher expression at 0 months than at 3 months

Figure: Screenshot of top returns of a differential search for genes with higher expression at 0 months than 3 months represented as a z-score heatmap ranging from green (below mean) to red (above mean).

Correlative Search

The correlative search function finds probes with expression profile similar to that of a 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 the results ranked in descending order.

The correlative search function can be accessed through the Web application or using the API.

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

Example:
Correlative search for probes with similar expression to NTNG1 probe MmuSTS.4647.1.S1_at over the cerebral cortex

Macrodissection Microarray

Experimental Overview and Metadata

The NHP Developmental Macrodissection Microarray Study is a genome-wide microarray profiling survey of 5 gross brain regions using rhesus macaque-specific DNA microarrays at four postnatal developmental stages.

Normalized microarray expression values can be downloaded in several ways:

All experimental data from this study is associated with the "Non-Human Primate Macro 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:

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

Example:

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

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

Each probe contains information about:

Each sample contains information about:

Differential Search

The differential search function finds 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 accessed through the Web application or using the API.

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

Example:
Differential search for genes with higher expression in "basal ganglia" than the "neocortex"

Example:
Differential search for genes with higher expression at 0 mo than 3 mo

Correlative Search

The correlative search function finds probes with expression profile similar to that of a 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.

The correlative search function can be accessed through the Web application or using the API.

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

Example:
Correlative search for probes with similar expression to NTNG1 probe MmuSTS.4647.1.S1_at over the cerebral cortex