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. The 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 with a Structure. For convenience, surveyed structures are grouped together in the "Developing Human - Transcriptome" StructureSet.

Typically, for each sample four types 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

Normalized expression values can be obtained by specifying:

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

Expression Type

"set"
parameter

"probe"
object

RNA-Seq RPKM values
summarized to the gene level

rna_seq_genes

Gene
(ensembl_id not null )

RNA-Seq RPKM values
summarized to the exon level

rna_seq_exons

GoExons

Exon microarray expression values
summarized to the gene level

exon_microarray_genes

Gene
(entrez_id not null )

Exon microarray expression values
summarized to the probeset level

exon_microarray_exons

AffymetriProbsets

RNA-Seq RPKM values summarized to the gene level

Example:

Download RNA-Seq expression values for samples from donor "H376.VI.52" associated with gene CARTPT

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

"probes":[
    {"id":1098278,
    "name":"ENSG00000164326",
    "gene-id":9463,
    "gene-symbol":"CARTPT","gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":"n/a","end-position":"n/a",
    "expression_level":["5.5566","4.9466","5.6331",...]}
    ],
"samples":[
    {"donor":{"id":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "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":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "structure":{"id":10185,"name":"ventrolateral prefrontal cortex","abbreviation":"VFC","color":"C2A335"},
     "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}},
     {"donor":{"id":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "structure":{"id":10278,"name":"anterior (rostral) cingulate (medial prefrontal) cortex","abbreviation":"MFC","color":"E26880"},
     "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}}, ...
     ],

Each probe (Gene) contains information about:

Each sample contains information about:

RNA-Seq RPKM values summarized to the exon level

Example:

Download RNA-Seq expression values for samples from donor "H376.VI.52" and all exons associated with gene CARTPT

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

"probes":[
    {"id":279330730,
    "name":"ENSG00000164326",
    "gene-id":1098278,
    "gene-symbol":"CARTPT",
    "gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":71014989,"end-position":71015279,
    "expression_level":["5.7282","4.8102","5.7152", ... ]},
    {"id":279330735,
    "name":"ENSG00000164326",
    "gene-id":1098278,"gene-symbol":"CARTPT",
    "gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":71015405,"end-position":71015790,
    "expression_level":["4.4128","3.8230","4.3135", ... ]},
    {"id":279330740,
    "name":"ENSG00000164326",
    "gene-id":1098278,"gene-symbol":"CARTPT",
    "gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":71016334,"end-position":71016875,
    "expression_level":["5.9593","5.4664","6.1137", ... ]}
    ],
"samples":[
    {"donor":{"id":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "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":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "structure":{"id":10185,"name":"ventrolateral prefrontal cortex","abbreviation":"VFC","color":"C2A335"},
     "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}},
     {"donor":{"id":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "structure":{"id":10278,"name":"anterior (rostral) cingulate (medial prefrontal) cortex","abbreviation":"MFC","color":"E26880"},
     "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}}, ...
     ],

Each probe (GoExon) contains information about:

Each sample contains information about:

Normalized exon microarray expression values summarized to the gene level

Example:

Download exon microarray expression values for samples from donor "H376.VI.50" associated with gene CARTPT

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

"probes":[
    {"id":9463,
    "name":"ENSG00000164326",
    "gene-id":9463,
    "gene-symbol":"CARTPT",
    "gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":"n/a","end-position":"n/a",
    "expression_level":["8.1073","5.9564","6.3102","7.0532","9.6157","7.1290","5.1168","4.4212","4.2779"],
    "z-score":["1.3547","0.0538","0.2678","0.7172","2.2670","0.7630","-0.4541","-0.8748","-0.9615"]}
    ],
"samples":[
    {"donor":{"id":12296,"name":"H376.VI.50","age":"4 mos","color":"80FF80"},
    "structure":{"id":10278,"name":"anterior (rostral) cingulate (medial prefrontal) cortex","abbreviation":"MFC","color":"E26880"},
    "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":10243,"name":"posterior (caudal) superior temporal cortex (area 22c)","abbreviation":"STC","color":"D670A0"},
    "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}}, ...
    ]

Each probe (Gene) contains information about:

Each sample contains information about:

Normalized exon microarray expression values summarized to a probeset level

Download exon microarray expression values for samples from donor "H376.VI.50" for all probesets associated with gene CARTPT

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

"probes":[
    {"id":280550735,
    "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":["8.1073","6.4681","6.3102","7.0532","9.4350","7.1290","5.1560","5.0550","4.9879"],
    "z-score":["1.4783","0.0367","-0.1021","0.5513","2.6458","0.6179","-1.1171","-1.2059","-1.2649"]},
    {"id":280550750,
    "name":"ENSG00000164326",
    "gene-id":9463,
    "gene-symbol":"CARTPT",
    "gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":71016613,"end-position":71016799,
    "expression_level":["10.1951","8.8021","7.7846","9.4317","11.8110","10.0210","6.1850","5.6075","4.5526"],
    "z-score":["1.2342","0.6566","0.2348","0.9177","1.9041","1.1620","-0.4284","-0.6678","-1.1052"]},
    ],
"samples":[
    {"donor":{"id":12296,"name":"H376.VI.50","age":"4 mos","color":"80FF80"},
    "structure":{"id":10278,"name":"anterior (rostral) cingulate (medial prefrontal) cortex","abbreviation":"MFC","color":"E26880"},
    "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":10243,"name":"posterior (caudal) superior temporal cortex (area 22c)","abbreviation":"STC","color":"D670A0"},
    "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}}, ...
    ]

Each probe (Gene) contains information about:

Each sample contains information about:

Differential Search

Differential search find "probes" that show the greatest difference in expression values 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 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::dev_human_differential parameters.

Example:

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

Figure: Screenshot of top returns of a differential search for genes with higher expression in the striatum than in the whole neural plate.

Example:

Differential search for genes with higher expression at 8-9 pcw than at 10-12 pcw over the whole "neural plate" for each of the four types of expression data.

Correlative Search

Correlative search finds "probes" with expression profile similar that of a to 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::dev_human_correlation parameters.

Example:

Correlative search for "probes" with similar expression to PVALB over the whole brain

PRENATAL LMD MICROARRAY

Experimental Overview and Metadata

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

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, sets of tiling probes were designed. This study uses the same chip design as the Human Brain Microarray Survey.

Each sampling site was associated with 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 "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":["5.6462","5.9486","3.1022"],
    "z-score":["2.4164","2.6249","0.6624"]},
    {"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":["2.8149","1.2956","1.7658"],
    "z-score":["0.8169","-0.9788","-0.4231"]}
    ],
"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 finds 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 accessed 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 in the transient structures of forebrain. The z-score heatmap shows enrichment in the thalamus relative to other brain regions.

Correlative Search

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

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

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

Example:
Correlative search for probes with similar expression to PVALB probe CUST_11451_PI416261804 over the whole neural plate

Figure: Screenshot of top returns of a correlative search for probes with similar expression to a PVALB probe with expression values displayed as a z-score heatmap.