The brain section - Protein profiles of different regions of the brain



This section provides comprehensive spatial profiling of the Brain, including overview of protein expression in the mammalian brain based on integration of data from human, pig and mouse. Transcriptomics data combined with affinity-based protein in situ localization down to single cell detail is available in this brain-centric sub atlas of the Human Protein Atlas. The data presented are for human genes and their one-to-one orthologues in pig and mouse. Gene summary pages provide the hierarchical expression landscape form 13 main regions of the brain to individual nuclei and subfields for every protein coding gene. For selected proteins, high content images are available to explore the cellular and subcellular protein distribution. In addition, the Brain section contains lists of genes with elevated expression in one or a group of regions to help the user identify unique protein expression profiles linked to physiology and function.

More information about the specific content and the generation and analysis of the data in this section can be found on the Methods Summary.

Learn about:

  • Expression levels for all human proteins in regions and subregions of the human brain
  • Expression levels for all proteins with human orthologs in regions and subregions of the pig and mouse brain
  • Brain enriched genes with higher expression in any of the regions of the brain compared to peripheral organs
  • Regional enriched genes with higher expression in a single or few regions of the brain
  • Cell-type and cell-compartment distribution of selected proteins in the human and mouse brain
  • Differences in gene expression between mammalian species

Additional information:

In addition to the data provided in the brain section there is also data on human retina and single cell data containing information on protein expression in human neuronal and non-neuronal cell-types in the central nervous system.


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 its complexity. Regional classification is perfomed in human, pig and mouse brain separately by comparing transcriptomic data summarized into 14 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 14 anatomical regions, providing regional classification of all genes based on RNA expression, indicating which proteins are elevated in one region compared to the other.


The brain is here divided into 13 defined anatomical regions, used for expression classification in individual regions of human, pig and mouse brain respectively.

For comparison of brain and peripheral organs, the highest normalized expression (nTPM) value of a brain region within GTEx data was used as representation of the brain. These values were used for comparison to the rest of the human body, defining the brain elevated genes from a whole body perspective.

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 2197 genes are classified as brain elevated and 97 genes were only detected in the brain. In total, 15331 of all human protein coding genes (n=20162) are detected in the human brain.

The regional classification of human brain is based on RNA seq analysis micropunch samples (Human Brain Tissue Bank - Semmelweis University, Hungary) including 190 regions, areas and subfields summarized in 13 main regions. Genes are classified based on detection above cut-off (1 nTPM) and regional distribution. Similar classification was also performed on pig and mouse for all human one-to-one orthologous genes.

The table below shows 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.


The brain RNA data was used to cluster genes according to their expression across brain regions. The clustering of 17832 genes expressed in brain tissues resulted in 56 expression clusters, which have been manually annotated to describe common features in terms of distribution, function and specificity. The result of the cluster analysis is presented as a UMAP based on gene expression, where each cluster has been summarized as colored areas containing most of the cluster genes.

Go to interactive expression cluster page