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Show complete data for human cells assay. The location(s) are highlighted in the illustration on the right.
Mainly localized to the nucleoplasm.
RNA cell categoryi
The cell lines in the Human Protein Atlas have been analyzed by RNA-seq to estimate the transcript abundance of each protein-coding gene. The RNA-seq data was then used to classify all genes according to their cell line-specific expression into one of six different categories, defined based on the total set of all TPM values in all analyzed cell lines.
Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence, or iv) not available.
Evidence at protein level
Main locationi
The main location is characterized by presence in all tested cell lines and/or increased intensity compared to other locations. It is highlighted in the illustration to the right. 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 analysis of GFP-tagged protein.
DATA RELIABILITY
Reliability scorei
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.
Below is an overview of RNA expression data generated in the HPA project. The analyzed cell lines are divided into 12 color-coded groups according to the organ they were obtained from. 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. The RNA-sequencing results generated in the HPA are reported as number of Transcripts per Kilobase Million (TPM). In the Human Protein Atlas a TPM value of 1.0 is defined as a treshhold for expression of the corresponding protein.
The cell lines in the Human Protein Atlas have been analyzed by RNA-seq to estimate the transcript abundance of each protein-coding gene. The RNA-seq data was then used to classify all genes according to their cell line-specific expression into one of six different categories, defined based on the total set of all TPM values in all analyzed cell lines.
Cell lines sorted after organ of phenotypic resemblance.
Cell lines sorted after biological source for establishment.
Cell lines sorted after the cell line category according to Cellosaurus.
Cell lines sorted on descending RNA expression.
Cell lines sorted alphabetically.
HUMAN CELLSi
The "human cells" section gives an overview about the subcellular location of the protein of interest obtained by indirect immunofluorescence microscopy, an antibody-based protein-visualization technique. The immunofluorescent analysis is carried out in three different cell lines, one of them always being U-2 OS. A selection of immunofluorescent images is displayed below. Three different organelle probes are displayed as different channels in the multicolor images - nucleus stained in blue, microtubules in red and ER in yellow. The antibody staining targeting the protein of interest is shown in green. By using the toggle channel buttons, the different channels can be turned on and off. For the selection of the images to compare, use the checkboxes next to the images at the bottom. Three images can be compared at a time. 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. For cell structure reference, visit the cell dictionary.
Summaryi
Summary of the immunofluorescent analysis in all studied cell lines with all tested antibodies.
Mainly localized to the nucleoplasm.
Main locationi
The main location is characterized by presence in all tested cell lines and/or increased intensity compared to other locations.
Nucleoplasm (enhanced)
Toggle channelsi
Three different organelle probes are displayed as different channels in the multicolor images - nucleus stained in blue, microtubules in red and ER in yellow. The antibody staining targeting the protein of interest is shown in green. By using the "toggle channels"-buttons, the different channels can be turned on and off. 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.
Low
High
G1
S
G2
M
N/A
Thumbnaili
Representative images for the assay. Three images can be compared at the same time. To change which images to compare, use the checkboxes next to the images below. 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.
Cell linei
Cell line used for analysis. Read more about the cell lines in the Human Protein Atlas.
Locationi
Location(s) annotated in the corresponding cell line.
Single-cell variationi
As the images in the Cell Atlas provide single cell resolution, variations in protein expression patterns from cell to cell can be observed. A single-cell variation can either be observed in the intensity of the immunofluorescent signal or in the spatial distribution pattern of the protein. This column contains information about whether and for which of the annotated locations a single-cell variation pattern was manually annotated.
Cell cycle dependent variationi
A likely cause for single-cell variation in the immunofluorescent images is cell cycle dependency. This column contains information about whether the manually observed cell-to-cell variation pattern correlates with cell cycle progression.
The siRNA validation section gives an overview of the siRNA downregulation assay performed for the antibody. For each HPA antibody, the siRNA downregulation assay is performed in duplicates with two different siRNAs. Only successful assays are included in the Atlas. Read more about siRNA validation. In the table at the top the siRNA validation score for the assay is shown together with the results from the statistical analysis of the analyzed images. The Relative Fluorescence Intensity (RFI) denotes the percentage of remaining staining intensity after siRNA downregulation. The boxplot on the top left is magnified when clicked, and illustrates the changes in fluorescent light intensity between siRNA treated and control (scrambled) samples. Also, the cell segmentation compartment, in which the changes in intensity have been measured, is noted here. siRNA transfected U-2 OS cells are immunofluorescently stained with the corresponding antibody. Images from the scrambled siRNA (negative control) well are displayed to the left and the images from one or two siRNA-assays are displayed to the right. 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. To change which images to compare, use the checkboxes next to the images at the bottom. Three images can be compared at a time. 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.
For each siRNA validation assay a validation score is assigned based on the decrease in antibody staining intensity upon target protein downregulation.
Enhanced: Significant downregulation > 25% by one siRNA and > 10% by the other.
Analysis performed ini
The cell segmentation 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
An siRNA designed specifically against the mRNA transcript corresponding to the protein targeted by the HPA-antibody.
RFIi
Relative Fluorescence Intensity (RFI) denotes the percentage of remaining staining intensity after siRNA down regulation. It is calculated by comparing cell population median staining intensities between siRNA down regulation and scrambled (negative control) samples.
70%
76%
p-valuei
The p-value is used to determine whether a result is statistically significant. It was calculated using the Wilcoxon rank sum test (Mann-Whitney). A p-value below 0.01 is considered significant.
< 0.01
< 0.01
Toggle channelsi
Three different organelle probes are displayed as different channels in the multicolor images - nucleus stained in blue, microtubules in red and ER in yellow. The HPA-antibody staining targeting the protein of interest is shown in green. By using the "toggle channels"-buttons, the different channels can be turned on and off. 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.
Low
High
G1
S
G2
M
N/A
Thumbnail 10xi
Representative immunofluorescent images that were acquired with a 10x objective after siRNA downregulation. Three images can be compared at the top of this section. To change which images to compare, use the checkboxes next to the images below. 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.
Thumbnail 40xi
Representative immunofluorescent images that were acquired with a 40x objective. Three images can be compared at the top of this section. To change which images to compare, use the checkboxes next to the images below. 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.
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.
The GFP section gives an overview of the colocalization of one or more antibodies with GFP-tagged target protein in HeLa cells. Read more about antibody validation by GFP colocalization. At the top of this section a selected image for each antibody is shown together with a validation summary for the antibody. A selection of immunofluorescent images using the antibody in cells expressing GFP-tagged target proteins as well as in untransfected HeLa cells is displayed below. The antibody staining, GFP and two organelle probes are displayed as different channels in the multicolor images. By using the "toggle channels"-buttons, the different channels can be turned on and off. To change which images to compare, use the checkboxes next to the images at the bottom. Three images can be compared at a time. 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. For cell structure reference, visit the cell dictionary.
Antibodyi
Antibody used for analysis. Clicking the antibody ID links to the antibody validation page.
Summary of the recombinant expression validation. Antibodies are analyzed in HeLa cell lines stably expressing GFP-tagged target protein. The target protein can be tagged at either the N- or C-terminal end of the target gene; for some genes both versions are available. For each GFP validation assay a validation score is assigned based on colocalization of the antibody staining and the GFP-tagged protein.
C-terminal tag BAC cell line: 6203 Enhanced: Antibody staining overlaps with GFP tagged protein
Toggle channelsi
Two different organelle probes are displayed as different channels in the multicolor images - nucleus stained in blue and microtubules in red. The HPA-antibody staining targeting the protein of interest is shown in green and the staining of the GFP-tagged protein in purple. By using the "toggle channels"-buttons, the different channels can be turned on and off. The intensity toggle shows the pixel intensity range in 16 different colors for the selected channel.
Low
High
G1
S
G2
M
N/A
Thumbnaili
Representative images for the assay. Three images can be compared at the same time. To change which images to compare, use the checkboxes next to the images below. 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.
Cell linei
Cell line used for analysis. Read more about the cell lines in the Human Protein Atlas.
BAC idi
Read more about the BAC cell lines by going to the Hyman lab, who created and supplied the BAC cell lines with an assigned BAC id. The untransfected HeLa control cells are referred to as "normal".
Tagi
The GFP construct can be tagged to the target protein at either the N- or C-terminal, for some genes both versions are available.
Location antibody stainingi
Subcellular location(s) annotated for the HPA-antibody.
Location tagged proteini
Subcellular location(s) annotated for the GFP-staining.
Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.
Gene name
HDAC1 (HGNC Symbol)
Synonyms
GON-10, HD1, RPD3L1
Description
Histone deacetylase 1 (HGNC Symbol)
Entrez gene summary
Histone acetylation and deacetylation, catalyzed by multisubunit complexes, play a key role in the regulation of eukaryotic gene expression. The protein encoded by this gene belongs to the histone deacetylase/acuc/apha family and is a component of the histone deacetylase complex. It also interacts with retinoblastoma tumor-suppressor protein and this complex is a key element in the control of cell proliferation and differentiation. Together with metastasis-associated protein-2, it deacetylates p53 and modulates its effect on cell growth and apoptosis. [provided by RefSeq, Jul 2008]
The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.
At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.
Under the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50). The region with the lowest possible identity is always selected for antigen design, with a maximum identity of 60% allowed for designing a single-target antigen (read more).
The curve in blue displays the predicted antigenicity i.e. the tendency for different regions of the protein to generate an immune response, with peak regions being predicted to be more antigenic.The curve shows average values based on a sliding window approach using an in-house propensity scale. (read more).
If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.
Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.
HDAC1-001
HDAC1-010
PROTEIN INFORMATIONi
The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.
The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.
The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.
The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
Enzymes ENZYME proteins Hydrolases Predicted intracellular proteins Plasma proteins FDA approved drug targets Small molecule drugs Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000118 [histone deacetylase complex] GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000785 [chromatin] GO:0000790 [nuclear chromatin] GO:0000976 [transcription regulatory region sequence-specific DNA binding] GO:0000978 [RNA polymerase II core promoter proximal region sequence-specific DNA binding] GO:0000980 [RNA polymerase II distal enhancer sequence-specific DNA binding] GO:0001047 [core promoter binding] GO:0001085 [RNA polymerase II transcription factor binding] GO:0001103 [RNA polymerase II repressing transcription factor binding] GO:0001106 [RNA polymerase II transcription corepressor activity] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0004407 [histone deacetylase activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005737 [cytoplasm] GO:0005829 [cytosol] GO:0006325 [chromatin organization] GO:0006338 [chromatin remodeling] GO:0006346 [methylation-dependent chromatin silencing] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006476 [protein deacetylation] GO:0007596 [blood coagulation] GO:0008134 [transcription factor binding] GO:0008284 [positive regulation of cell proliferation] GO:0009913 [epidermal cell differentiation] GO:0010629 [negative regulation of gene expression] GO:0010870 [positive regulation of receptor biosynthetic process] GO:0016032 [viral process] GO:0016569 [covalent chromatin modification] GO:0016575 [histone deacetylation] GO:0016580 [Sin3 complex] GO:0016581 [NuRD complex] GO:0016787 [hydrolase activity] GO:0019213 [deacetylase activity] GO:0019899 [enzyme binding] GO:0031492 [nucleosomal DNA binding] GO:0032041 [NAD-dependent histone deacetylase activity (H3-K14 specific)] GO:0032922 [circadian regulation of gene expression] GO:0033558 [protein deacetylase activity] GO:0033613 [activating transcription factor binding] GO:0042475 [odontogenesis of dentin-containing tooth] GO:0042733 [embryonic digit morphogenesis] GO:0042826 [histone deacetylase binding] GO:0043044 [ATP-dependent chromatin remodeling] GO:0043066 [negative regulation of apoptotic process] GO:0043234 [protein complex] GO:0043922 [negative regulation by host of viral transcription] GO:0044212 [transcription regulatory region DNA binding] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0047485 [protein N-terminus binding] GO:0048511 [rhythmic process] GO:0051059 [NF-kappaB binding] GO:0060766 [negative regulation of androgen receptor signaling pathway] GO:0060789 [hair follicle placode formation] GO:0061029 [eyelid development in camera-type eye] GO:0061198 [fungiform papilla formation] GO:0070491 [repressing transcription factor binding] GO:0070932 [histone H3 deacetylation] GO:0070933 [histone H4 deacetylation] GO:0090090 [negative regulation of canonical Wnt signaling pathway] GO:1901796 [regulation of signal transduction by p53 class mediator] GO:1904837 [beta-catenin-TCF complex assembly]
The Human Protein Atlas project is funded
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