ACKNOWLEDGMENTS PROTEIN CLASSES PROTEIN EVIDENCE EDUCATIONAL VIDEOS DOWNLOADABLE DATA PUBLICATION DATA RELEASE HISTORY ANTIBODY AVAILABILITY PRIVACY STATEMENT LICENCE & CITATION This resource 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 resource 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 resource can be found on the Methods Summary . 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 resource 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. Recent development in transcriptomics technologies (detection of RNA) enable quantification of RNA content of tissues and single cells. Especially spatial transcriptomics technologies that detect both transcripts and their spatial location have become available for researchers. The major breakthroughs in the field of spatial transcriptomics have been the spatial resolution (< 1 micrometer) and the possibilities to simultaneously detect all transcripts (genome wide). The major advantages of high-resolution spatial transcriptomics methods compared to single cell or single nuclei transcriptomics are the ability to investigate all cells including rare cells in a single tissue section while maintaining information on the cellular environment and neighboring cells. In the brain section you can now find information of protein coding transcripts in the 5 main cell-types of the human cerebral cortex. More information about spatial transcriptomics you can find in this knowledge resource and the cerebellum and cerebral cortex resources Human cortex 5 cell-types spatial transcriptomics

The Brain Atlas includes data from different species (human, pig and mouse) and different regions of the brain (bellow). There are several different cell types in the brain, illustrated in a specific summary page. Retina and pituitary gland both share developmental origin with the brain and is also included in the brain atlas. Each symbol bellow is clickable and will redirect to the selected summary page. 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. The Brain Atlas includes data from different species and regions of the brain, illustrated with a specific color throughout the brain atlas illustrations. Each symbol and region name is clickable and will redirect to the selected regional summary page. 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. This paragraph provides an overview of proteins elevated in brain from a whole body perspective and proteins elevated in regions of the brain from a whole brain perspective. 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 2227 genes are classified as brain elevated and 99 genes were only detected in the brain. In total, 15348 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. Human Pig Mouse Brain region Detected Regionally elevated Detected Regionally elevated Detected Regionally elevated Cerebral cortex 16993 180 14138 109 12540 55 Cerebellum 16305 162 13564 165 12054 182 Olfactory bulb n/a n/a 13937 89 12410 158 Basal ganglia 16576 83 14256 157 12890 185 Thalamus 16612 57 13915 31 12557 60 Hypothalamus 16623 110 14061 45 12528 98 Midbrain 16618 87 14335 114 12397 47 White matter 16727 67 13612 4 12565 62 Amygdala 16293 22 13954 49 12416 38 Choroid plexus 15744 371 n/a n/a n/a n/a Pons 16747 96 13950 41 12587 98 Medulla oblongata 16792 90 13995 37 12587 98 Hippocampal formation 16266 45 14236 121 12623 91 Spinal cord 16208 45 14089 236 n/a n/a 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 here ). 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 The UMAP was generated by clustering genes based on expression patterns. The colored areas represent the area in the UMAP where most of the genes of each cluster reside. Click on a cluster or Go to interactive expression cluster page to view an interactive UMAP and details about all cluster annotations. 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 The Human Protein Atlas DOWNLOADABLE DATA LICENCE & CITATION