The Brain Atlas



The Brain Atlas explores the protein expression in the mammalian brain by visualization and integration of data from three mammalian species (human, pig and mouse). Transcriptomics data combined with affinity-based protein in situ localization down to single cell detail is here available in a brain-centric sub atlas of the Human Protein Atlas. The data focuses on human genes and one-to-one orthologues in pig and mouse. Each gene is provided with a summary page, showing available expression data (mRNA) for summarized regions of the brain as well as protein location for selected targets. High resolution staining images as well as expression data for the individual sub regions are all available for exploring the brain, the most complex organ.


Gene classification based on expression in tissue types representing the whole human body enables the description of brain elevated proteins. Regional expression data is used for in depth classification of the brain, highlighting the complexity. Regional classification is perfomed in human, pig and mouse brain separately by comparing transcriptomic data summarized into 10 main regions of each mammalian brain. The regional classification in human brain is also compared to the whole-body expression. The combination of transcriptomic data and antibody-based protein profiling is investigated on separate summary pages as a platform for further exploring the brain proteome.

Explore the various regions of the brain

Brain samples are grouped into 10 anatomical regions, providing regional classification of >16,000 genes based on RNA expression, indicating which proteins are elevated in one region compared to the other.


The brain is here divided into 10 defined anatomical regions, used for expression classification in individual regions of human, pig and mouse brain respectively.

The highest normalized expression (NX) value within the 10 regions as well as spinal cord and corpus callosum in human brain is also used as representation of the brain in comparison to the rest of the human body, defining the brain elevated genes on a whole body level.

All human protein-coding genes are categorized according to detection above cut of (tissue detection category) as well as relative abundance between tissue types (tissue specificity category).

A number of 2587 genes are classified as brain elevated and 33 genes were only detected in the brain. In total 16227 of all human protein coding genes (N=19670) are detected in the human brain.

The regional classification of human brain is based on available FANTOM5 and GTEx expression data and includes regional classification of 17229 protein-coding genes (15157 genes are classified as detected). Expression data from pig and mouse brain are also used for regional classification, for human one-to-one orthologous genes. The table below show the number of genes detected above cut off in the different brain regions as well as the number of genes classified as elevated in each region. More details about the different regions can be found at the respective regional summary page.

To complement transcriptomic data, antibody-based tissue profiling is utilized to locate proteins in situ of both human and mouse brain (read more about the technical background under assay and annotation). Protein profiles are found at the individual gene summary pages, click examples or search for your favorite target to explore the brain expression and protein location.







Selected examples of protein location in human or mouse brain.