The Subcellular resource - A subcellular map of the human proteome

Subcellular methods

The subcellular resource of the Human Protein Atlas provides high-resolution insights into the expression and spatiotemporal distribution of proteins encoded by 13603 genes (67% of the human protein-coding genes), as well as predictions for an additional 3459 secreted- or membrane proteins, covering a total of 17062 genes (85% 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 standard cell lines, selected from a panel of 42 cell lines used in the subcellular resource. For some genes, the protein has also been stained in up to three ciliated cell lines, induced pluripotent stem cells (iPSCs) and/or in human sperm cells. Upon image analysis, the subcellular localization of the protein has been classified into one or more of 49 different organelles and subcellular structures. In addition, the resource 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 resource 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 resouce, 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 standard human cell lines, including ciliated cells and iPSCs.
The subcellular distribution of proteins in human sperm.
The proteomes of different organelles and subcellular structures.
Single-cell variability in the expression levels and/or localizations of proteins.

EXPLORE THE SUBCELLULAR 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 interactive subcellular location UMAP 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 study the high-dimensional protein localization data that makes up the subcellular resource, 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. Click on the UMAP or explore the interactive vesion of the subcellular 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 cellular and organelle proteome chapters is a collection of interactive pages providing conceptual overviews, compilations and analyses of the data generated within the subcellular resource. Discover the proteomes of particular organelles, the cell cycle-dependent proteome and transcriptome, the multilocalizing proteome and the metabolic proteome in knowledge summaries, providing different perspectives on the distribution of proteins in human cells. 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.
Multilocalizing proteome Organelle proteome Cell cycle dependent transcriptome and proteome Metabolic proteome
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
Primary Cilium	Primary Cilium - Basal body - Primary cilium - Primary cilium tip - Primary cilium transition zone
Secretory	Secreted Proteins - Secreted proteins
Sperm	Sperm - Acrosome - Annulus - Calyx - Connecting piece - End piece - Equatorial segment - Flagellar centriole - Mid piece - Perinuclear theca - Principal piece

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 different organelles and compartments, and get familiar with their unique structures and functions.