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

THE BRAINⁱ

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 13 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.

Human brain

Mouse brain

Pig brain

Brain cell types

Retina

Pituitary gland

Choroid plexus

BRAIN REGIONSⁱ

Explore the various regions of the brain

Brain samples are grouped into 13 anatomical regions, providing regional classification of all genes based on RNA expression, indicating which proteins are elevated in one region compared to the other.

Cerebral cortex
Olfactory bulb
Hippocampal formation
Amygdala
Basal ganglia
Thalamus

	Hypothalamus
	Midbrain
	Cerebellum
	Pons
	Medulla oblongata
	Spinal cord
	White matter

BRAIN SUMMARY

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

The highest normalized expression (nTPM) value within the 13 regions was also used as representation of the brain in 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 2685 genes are classified as brain elevated and 202 genes were only detected in the brain. In total, 16465 of all human protein coding genes (n=20090) are detected in the human brain.

The regional classification of human brain is based on RNA seq analysis of 1324 micropunch samples (Human Brain Tissue Bank - Semmelweis University, Hungary) including >200 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.

	Human		Pig		Mouse
Brain region	Detected	Regionally elevated	Detected	Regionally elevated	Detected	Regionally elevated
Cerebral cortex	15332	409	13194	96	12290	55
Hippocampal formation	14378	182	13285	106	12373	91
Amygdala	14373	110	13015	41	12166	38
Basal ganglia	14685	199	13274	143	12629	183
Thalamus	14704	89	12896	25	12304	61
Hypothalamus	14309	78	13044	42	12272	97
Midbrain	14409	80	13335	106	12147	45
Pons	14546	83	12943	39	12331	97
Cerebellum	14362	322	12560	155	11817	178
Medulla oblongata	14604	80	13010	34	12331	97
Spinal cord	13529	35	13109	214	n/a	n/a
White matter	14793	112	12629	3	12305	61

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.

SLC1A3
NECAB1
HOMER3
PDYN
NCDN
SLC2A1

Selected examples of protein location in human or mouse brain.