A subcellular map of the human proteome

The Subcellular section of the Human Protein Atlas provides high-resolution insights into the expression and spatiotemporal distribution of proteins encoded by 13041 genes (65% of the human protein-coding genes). For each gene, the subcellular distribution of the protein has been investigated by immunofluorescence (ICC-IF) and confocal microscopy in up to three different cell lines, selected from a subset of 36 of the cell lines found in the Cell Line Section. Upon image analysis, the subcellular localization of the protein has been classified into one or more of 35 different organelles and fine subcellular structures. In addition, the section includes an annotation of genes that display single-cell variation in protein expression levels and/or subcellular distribution, as well as an extended analysis of cell cycle dependency of such variations.

The Subcellular Section offers a database for detailed exploration of individual genes and proteins of interest, as well as for systematic analysis of proteomes in a broader context. More information about the content of the section, as well as the generation and analysis of the data, can be found in the Methods Summary.

Learn about:

  • the subcellular distribution of proteins in human cell lines.
  • the proteomes of different organelles and subcellular structures.
  • single-cell variability in the expression levels and/or localizations of proteins.


Uniform Manifold Approximation and Projection (UMAP) is an analytical technique for reducing the dimensionality of a data set (Becht E et al. (2018)). The Cell Atlas UMAP Explorer has been generated using the large collection of confocal microscopy images showing the subcellular localization patterns of human proteins. This tool provides a new way to visualize and explore the highly dimensional protein localization data that makes up the Cell Atlas, projected in a two- or three dimensional space. By coloring the data points, each representing one image, according to subcellular localization(s) it is evident that images of proteins localizing to the same compartment tend to cluster together. Overlaying the UMAP projection with different data can allow you to find new features, and identify interesting groups of genes, in a large and complex data set. Explore the interactive vesion of the subcellular section location UMAP here.


Actin filaments
Centriolar satellite
Cleavage furrow
Cytokinetic bridge
Cytoplasmic bodies
Focal adhesion sites
Intermediate filaments
Microtubule ends
Midbody ring
Mitotic spindle
Rods & Rings


Mitotic chromosome
Nuclear bodies
Nuclear membrane
Nuclear speckles
Nucleoli fibrillar center
Nucleoli rim

Endomembrane system

Cell Junctions
Endoplasmic reticulum
Golgi apparatus
Lipid droplets
Plasma membrane

The Human Cellular and Organelle Proteome chapters are a collection of interactive pages providing conceptual overviews, compilations and analyses of the data generated within the Subcellular Section. Discover the Organelle proteome, the Cell cycle-dependent proteome and the Multilocalizing proteome in chapters providing different perspectives of the distribution of proteins in human cells. You can also find information about and analyses of each of the individual proteomes of the organelles and subcellular structures classified within the Subcellular Section, together with beautiful example images. The chapters can serve as an educational resource, but also as a starting point for deeper exploration of the fascinating spatiotemporal complexity of protein expression and distribution in human cells.

Nuclear membrane
- Nuclear membrane
- Nucleoli
- Nucleoli fibrillar center
- Nucleoli rim
- Kinetochore
- Mitotic chromosome
- Nuclear bodies
- Nuclear speckles
- Nucleoplasm
Actin Filaments
- Actin filaments
- Cleavage furrow
- Focal adhesion sites
- Centriolar satellite
- Centrosome
- Aggresome
- Cytoplasmic bodies
- Cytosol
- Rods & rings
Intermediate Filaments
- Intermediate filaments
- Cytokinetic bridge
- Microtubule ends
- Microtubules
- Midbody
- Midbody ring
- Mitotic spindle
- Mitochondria
Endomembrane system
Endoplasmic Reticulum
- Endoplasmic reticulum
Golgi Apparatus
- Golgi apparatus
Plasma Membrane
- Cell junctions
- Plasma membrane
- Endosomes
- Lipid droplets
- Lysosomes
- Peroxisomes
- Vesicles
Secreted proteins
- Secreted proteins

A Journey through the Cell

Join us on an inspiring journey through the human cell; the basic structural and functional unit of the human body and the home for many of our proteins. This video uses comprehensive animated graphics and microscopy images from the Subcellular section to give you an overview of the inner universe of a human cell. Travel through a world of organelles and subcellular compartments, and get familiar with their basic structures and unique functions.