All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions.
Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached.
Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s).
The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.
Number of protein-coding transcripts from the gene as defined by Ensembl.
HUMAN PROTEIN ATLAS INFORMATIONi
Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Main subcellular location(s) and reliability score(s) for the encoded protein(s) in human cells. The main location(s) may be characterized by presence in all tested cell lines and/or ihigher staining intensity compared to the potential additional location(s). If available, links to overrepresentation analyses in Reactome, a free, open-source, curated and peer reviewed biological pathway database, are provided. An analysis is done for the corresponding gene set of the proteome localizing to the main and additional locations of the protein on this page, respectively.
A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data.
Variation in transcript expression is correlated to the cell cycle.
Overall gene reliability score for the subcellular location(s) of the encoded protein(s). A reliability score is set for all genes and indicates the level of reliability of the analyzed protein expression pattern based on available protein/RNA/gene characterization data. The reliability of the annotated protein expression data is also scored depending on similarity in immunostaining patterns and consistency with available experimental gene/protein characterization data in the UniProtKB/Swiss-Prot database.
Overview of RNA expression levels in different cell lines analyzed in the Human Protein Atlas. The RNA-sequencing results generated in the HPA are reported as normalized transcript per million (nTPM) values. In the Human Protein Atlas a nTPM value of 1.0 is defined as a threshold for expression of the corresponding protein. The cell lines are divided into color-coded groups according to their origin in the human body. By clicking the toolbars in the top right corner it is possible to sort the cell lines in the chart by different criteria: the organ and the origin that the cell line was obtained from, the category of the cell line according to cellosaurus, alphabetically or by descending RNA expression. Detailed information about a specific cell line can be accessed by hovering over the corresponding bar in the chart.
RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines.
Cell lines ordered by organ of phenotypic resemblance.
Cell lines ordered by biological source for establishment order.
Cell lines ordered by category according to Cellosaurus.
Cell lines ordered by descending RNA expression order.
Cell lines in alphabetically order.
Assay for determining the subcellular location of encoded protein(s) by indirect immunofluorescence microscopy. The antibody-based staining is generally carried out in U2OS and two additional cell lines, selected based on RNA expression. Representative multi-color images showing the protein of interest in green are displayed below. The images also include markers for the nucleus (blue), microtubules (red) and ER (yellow). All images are clickable for an enlarged view. For cell structure reference, visit the cell dictionary.
Summary of the subcellular location, based on the immunofluorescent analysis in all studied cell lines and with all tested antibodies.
Localized to the nucleoplasm.
Main subcellular location(s) and reliability score(s) for the encoded protein(s) in human cells. The main location(s) may be characterized by presence in all tested cell lines and/or higher staining intensity compared to the potential additional location(s).
Buttons for turning on and off the different channels in the multi-color images. The intensity toggle shows the pixel intensity range in 16 different colors for the selected channel. The object toggle shows the computational segmentation of the cells used for further analysis in the HPA project. For samples where cell cycle dependency for the protein is suggested according to a correlation assay the predicted cell cycle position of each cell is displayed when using the object toggle.
Minatures of all available images. The checkboxes can be used to select which three images to compare in the window above. All images are also clickable for an enlarged view. The selected image will appear in large size and miniature images with all other staining results for this gene will be listed at the top left of the image. The selected miniature image has an orange overlay.
Antibody used for analysis. Clicking the antibody ID links to the antibody validation page.
Cell line used for analysis. Read more about the cell lines in the Human Protein Atlas.
Cell line RNA Expression (nTPM)i
RNA expression level in the cell line based on normalised RNA sequencing data. Genes with a value above 1 NX are considered to be expressed.
observed single-cell variation(s) in the staining pattern. Variation in protein expression levels can be observed as varaiations in the intensity of the immunofluorescent signal, while spatial variations can be observed asvariations in subcellular distribution of the protein.
Assays for determining cell cycle dependency of RNA and protein expression, based on stainings in the U-2 OS FUCCI (Fluorescence Ubiquitination Cell Cycle Indicator) cell line, or a computational model for cell cycle position, or localization to cell cycle dependent compartments (e.g. mitotic spindle, cytokinetic bridge).
Variation in transcript expression is correlated to the cell cycle.
RNA expression peak phase
RNA expression across cell cyclei
Assay for determining RNA expression level and cell cycle phase in single cells by single-cell RNA sequencing of the U-2 OS FUCCI cell line. Normalized RNA expression in individual cells is plotted along a linear representation of cell cycle pseudotime, as determined from the fluorescence intensities of the cell cycle markers.