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GENERAL INFORMATIONi
General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Gene namei
Official gene symbol, which is typically a short form of the gene name, according to HGNC.
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.
5
HUMAN PROTEIN ATLAS INFORMATIONi
Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Summaryi
Annotated subcellular location(s) for the encoded protein(s) based on the human cells assay. The location(s) are highlighted in the illustration on the right.
Mainly localized to the nucleoplasm. In addition localized to the nuclear bodies & midbody ring.
RNA cell specificityi
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.
Low cell line specificity
RNA cell distributioni
RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines.
Detected in all
Protein evidencei
Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.
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.
Additonal subcellular location(s) for the encoded protein(s) in human cells. The additional location(s) may not be present i all cell lines and may have lower staining intensity compared to the main 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.
The location(s) are Enhanced based on siRNA mediated gene silencing.
SINGLE CELL VARIATIONi
Summary of single cell variations on RNA and protein level based on data generated within the Human Protein Atlas project.
Single-cell variationi
Single-cell variations of protein expression or distribution observed within single images in human cells. 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.
Single-cell variation in protein expression observed.
Cell cycle dependencyi
Cell-cycle dependance of single-cell varations in RNA and/or protein expression as observed in an additional assay for characterizing single-cell varations. "NA" indicates a lack of such data.
The protein is localized to mitotic structures and is thus associated with the cell-cycle. Variation in transcript expression is not correlated to the cell cycle across interphase.
DATA RELIABILITYi
Overall reliability score for the subcellular location(s) of the protein(s) in human cells, and summary of the antibodies used for immunostainings.
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 NX values. In the Human Protein Atlas a NX value of 1.0 is defined as a threshhold 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.
HUMAN CELLSi
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.
Mainly localized to the nucleoplasm. In addition localized to the nuclear bodies & midbody ring.
Main locationi
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).
Nucleoplasm (enhanced)
Additional locationi
Additonal subcellular location(s) for the encoded protein(s) in human cells. The additional location(s) may not be present i all cell lines and may have lower staining intensity compared to the main location(s).
Nuclear bodies (enhanced), Midbody ring (approved)
Toggle channelsi
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.
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Thumbnaili
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.
Antibodyi
Antibody used for analysis. Clicking the antibody ID links to the antibody validation page.
Cell linei
Cell line used for analysis. Read more about the cell lines in the Human Protein Atlas.
Cell line RNA Expression (NX)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.
Cell-cycle dependance of observed single-cell varations in RNA and/or protein expression as observed in an additional assay for characterizing single-cell varations.
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).
The protein is localized to mitotic structures and is thus associated with the cell-cycle. Variation in transcript expression is not correlated to the cell cycle across interphase.
Locationi
Subcellular location of the protein(s) in U-2 OS FUCCI.
Midbody ring
Intensity variationi
Location(s) where a cell-to-cell variation correlates with cell cycle progression.
Midbody ring
Protein expression across cell cyclei
Assay for determining protein expression level and cell cycle phase in single cells by indirect immunofluorescence microscopy in the U-2 OS FUCCI cell line. The protein of interest is shown in yellow and microtubules in blue. U-2 OS FUCCI cells express two fluorescently tagged cell cycle markers, CDT1 during G1 phase (red) and Geminin during S and G2 phases (green). These markers are co-expressed during the G1-S transition. Protein expression in individual cells, as determined from the fluorescence intensity of the protein of interest, is plotted along a linear representation of cell cycle pseudotime, as determined from the fluorescence intensities of the cell cycle markers.
Buttons for turning on and off the different channels in the multi-color images.
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.
siRNA VALIDATIONi
Assay for validating subcellular location as determined by immunofluorescence by siRNA-mediated downregulation of gene expression. The top section shows a summary of the results of the siRNA validation assay. The box plot shows the Relative Fluorescence Intensity (RFI, i.e. percentage of remaining staining intensity after siRNA downregulation) in siRNA treated and negative control (scrambled) samples. Representative images of the negative control cells are displayed to the left and representative images of siRNA-treated cells are displayed to the right. All images are 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.
Antibodyi
Antibody used for analysis. Clicking the antibody ID links to the antibody validation page.
Enhanced: Significant downregulation > 25% by one siRNA.
Analysis performed ini
Compartment in which the changes in intensity have been measured. Depending on the original staining of the HPA antibody, a segmentation region covering either the nucleus, cytoplasm or the whole cell is used in the statistical analysis. Additionally it is noted whether the statistical analysis was performed in the 10x or 40x images.
Nuclear region of segmented cells in 10x-images
siRNA 2i
The siRNA validation assay is performed using two different siRNAs targeted against each gene. Results are only shown for siRNAs that mediate a down-regulation in protein expression as determined by immunofluorescence.
RFIi
Median Relative Fluorescence Intensity (RFI) after siRNA-mediated down regulation of gene expression when comparing siRNA treated cells with negative control (scrambled) cells.
42%
p-valuei
p-value calculated using a Wilcoxon rank sum test (Mann-Whitney) for the difference in staining intensity in siRNA-treated and negative control cells. A p-value below 0.01 is considered statistically significant.
< 0.01
Antibodyi
Antibody used for analysis. Clicking the antibody ID links to the antibody validation page.
Enhanced: Significant downregulation > 25% by both siRNA:s.
Analysis performed ini
Compartment in which the changes in intensity have been measured. Depending on the original staining of the HPA antibody, a segmentation region covering either the nucleus, cytoplasm or the whole cell is used in the statistical analysis. Additionally it is noted whether the statistical analysis was performed in the 10x or 40x images.
Nuclear region of segmented cells in 10x-images
siRNA 1i
An siRNA designed specifically against the mRNA transcript corresponding to the protein targeted by the HPA-antibody.
siRNA 2i
The siRNA validation assay is performed using two different siRNAs targeted against each gene. Results are only shown for siRNAs that mediate a down-regulation in protein expression as determined by immunofluorescence.
RFIi
Median Relative Fluorescence Intensity (RFI) after siRNA-mediated down regulation of gene expression when comparing siRNA treated cells with negative control (scrambled) cells.
20%
26%
p-valuei
p-value calculated using a Wilcoxon rank sum test (Mann-Whitney) for the difference in staining intensity in siRNA-treated and negative control cells. A p-value below 0.01 is considered statistically significant.
< 0.01
< 0.01
Toggle channelsi
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 antibody and intensity channel toggle can be used to further illustrate the intensity downregulation when comparing images from scrambled and targeting siRNA samples in the images. The object toggle shows the segmentation compartment in which the change in intensity after siRNA downregulation was measured.
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Thumbnail 10xi
Minatures of all available images acquired with a 10x objective after siRNA downregulation. 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.
Thumbnail 40xi
Minatures of all available images acquired with a 40x objective after siRNA downregulation. 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.
Antibodyi
Antibody used for analysis. Clicking the antibody ID links to the antibody validation page.
Samplei
siRNA that was used for the analysis.
Cell linei
Cell line used for analysis. Read more about the cell lines in the Human Protein Atlas.