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
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.
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.