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.


EXPLORE THE SUBCELLULAR SECTION LOCATION UMAP

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.

Cytoplasm

Actin filaments
Aggresome
Centriolar satellite
Centrosome
Cleavage furrow
Cytokinetic bridge
Cytoplasmic bodies
Cytosol
Focal adhesion sites
Intermediate filaments
Microtubule ends
Microtubules
Midbody
Midbody ring
Mitochondria
Mitotic spindle
Rods & Rings
Multilocalizing

Nucleus

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

Endomembrane system

Cell Junctions
Endoplasmic reticulum
Endosomes
Golgi apparatus
Lipid droplets
Lysosomes
Peroxisomes
Plasma membrane
Vesicles
CELLULAR & ORGANELLE PROTEOMES

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.

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