Allen Brain Atlas API

The BrainSpan Atlas of the Developing Human Brain is a foundational resource for studying transcriptional mechanisms involved in human brain development. Data includes:

From the API, you can:

Download expression values
Query the correlative and differential search services

Developmental Transcriptome

Experimental Overview and Metadata

The Developmental Transcriptome Study is a broad developmental survey of gene expression in specific brain regions using RNA sequencing and exon microarray techniques. The survey profiles up to sixteen targeted cortical and subcortical structures across the full course of human brain development, spanning pre- and postnatal-development in both males and females.

Each sampling site is associated to a Structure. 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.

Typically, for each sample four typs of expression values are available:

Normalized expression values can be downloaded in several ways:

All experimental data from this study is associated with the "Developing Human Transcriptome" Product. All gene, exon, probeset, donor and sampling site information can be accessed through the API using RMA queries.

Examples:

Downloading Expression Values

Differential Search

Correlative Search

Prenatal LMD Microarray

Experimental Overview and Metadata

The Prenatal LMD Microarray Study is a genome-wide microarray data profiling gene expression in finely dissected regions spanning the entire prenatal human brain and isolated using laser capture microdissection.

RNA isolated from each sample area was hybridized to a custom Agilent 8x60k microarray chip to measure gene expression over the transcriptome. All least two different probes were available for 93% of genes. Probes were located on different exons as much as possible when multiple probes were available for a gene. For 60 genes, a set of tiling probes were probes was designed. This study uses the same chip design as the Human Brain Microarray Survey.

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:

All experimental data from this study is associated with the "Developing Human Prenatal 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::dev_human_microarray_expression parameters.

Example:

Download expression values for donor "H376.IIIA.02" in structure "cerebellar cortex" for all probes associated with gene SLC6A.

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

"probes":[
    {"id":1023146,
    "name":"A_23_P358345",
    "gene-id":6494,
    "gene-symbol":"SLC6A2",
    "gene-name":"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2",
    "entrez-id":6530,"chromosome":"16","start-position":"n/a","end-position":"n/a",
    "expression_level":["5.6548","5.9550","3.1075"],
    "z-score":["2.4279","2.6347","0.6723"]},
    {"id":1023147,
    "name":"CUST_16472_PI416261804",
    "gene-id":6494,"gene-symbol":"SLC6A2",
    "gene-name":"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2",
    "entrez-id":6530,"chromosome":"16","start-position":"n/a","end-position":"n/a",
    "expression_level":["2.8128","1.2962","1.7661"],
    "z-score":["0.8252","-0.9664","-0.4113"]}
    ],
"samples":[
    {"donor":{"id":12840,"name":"H376.IIIA.02","age":"15 pcw","color":"0080FF"},
    "structure":{"id":10658,"name":"cerebellar vermis","abbreviation":"CBV","color":"76A2D5"},
    "top_level_structure":{"id":10657,"name":"cerebellar cortex","abbreviation":"CBC","color":"89ADDB"}},
    {"donor":{"id":12840,"name":"H376.IIIA.02","age":"15 pcw","color":"0080FF"},
    "structure":{"id":12384,"name":"paravermis of cerebellum","abbreviation":"CBPV","color":"4A8ECC"},
    "top_level_structure":{"id":10657,"name":"cerebellar cortex","abbreviation":"CBC","color":"89ADDB"}},
    {"donor":{"id":12840,"name":"H376.IIIA.02","age":"15 pcw","color":"0080FF"},
    "structure":{"id":12390,"name":"lateral hemisphere of cerebellum","abbreviation":"CBL","color":"4A8ECC"},
    "top_level_structure":{"id":10657,"name":"cerebellar cortex","abbreviation":"CBC","color":"89ADDB"}}
    ]

Each probe contains information about:

Each sample contains information about:

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.

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_microarray_differential parameters.

Example:
Differential search for genes with higher expression in "thalamus" than the "transient structures of forebrain"

Figure: Screenshot of top returns of a differential search for genes with higher expression in the thalamus than the cerebral cortex. Z-score heatmap shows enrichment (red) in the thalamus (structure color: light green) compare to other brain regions.

Correlative Search