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RNA category is based on mRNA expression levels in the analyzed samples (RNA assay description). The categories include: tissue/cell line enriched, group enriched, tissue/cell line enhanced, expressed in all, mixed and not detected. RNA category is calculated separately for The Cancer Genome Atlas (TCGA) data from cancer tissues and internally generated Human Protein Atlas (HPA) data from normal tissues and cell lines.
TCGA (cancer tissue):
Expressed in all
HPA (cell line):
Expressed in all
HPA (normal tissue):
Expressed in all
Protein evidencei
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
Protein expression normal tissuei
A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation.
"Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile.
Cytoplasmic expression in most cell types, most abundant in renal tubules and cells in seminiferus ducts.
IMMUNOHISTOCHEMISTRY DATA RELIABILITY
Data reliability descriptioni
Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.
Antibody staining mainly not consistent with RNA expression data.
Reliability score - normal tissuesi
Reliability score (score description), divided into Enhanced, Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between antibody staining pattern, available RNA-Seq and gene/protein characterization data, as well as similarity between independent antibodies targeting the same protein.
Kaplan-Meier plots for all cancers where high expression of this gene has significant (p<0.001) association with patient survival are shown in this summary. Whether the prognosis is favourable or unfavourable is indicated in brackets. Each Kaplan-Meier plot is clickable and redirects to a detailed page that includes individual expression and survival data for patients with the selected cancer.
RNA expression overview shows RNA-seq data from The Cancer Genome Atlas (TCGA).
TCGA dataseti
RNA-seq data in 17 cancer types are reported as median FPKM (number Fragments Per Kilobase of exon per Million reads), generated by the The Cancer Genome Atlas (TCGA). RNA cancer tissue category is calculated based on mRNA expression levels across all 17 cancer tissues and include: cancer tissue enriched, cancer group enriched, cancer tissue enhanced, expressed in all, mixed and not detected. To access cancer specific RNA and prognostic data, click on the cancer name. The cancer types are color-coded according to which type of normal organ the cancer originates from.
Antibody staining in 20 different cancers is summarized by a selection of four standard cancer tissue samples representative of the overall staining pattern. From left: colorectal cancer, breast cancer, prostate cancer and lung cancer. An additional fifth image can be added as a complement. The assay and annotation is described here. Note that samples used for immunohistochemistry by the Human Protein Atlas do not correspond to samples in the TCGA dataset.
For each cancer, color-coded bars indicate the percentage of patients (maximum 12 patients) with high and medium protein expression level. The cancer types are color-coded according to which type of normal organ the cancer originates from. Low or not detected protein expression results in a white bar. Mouse-over function shows details about expression level and normal tissue of origin. The images and annotations can be accessed by clicking on the cancer name or protein expression bar. If more than one antibody is analyzed, the tabs at the top of the staining summary section can be used to toggle between the different antibodies.
Seminomas and several cases of carcinoids, colorectal and breast cancers showed moderate cytoplasmic immunoreactivity. Other cancer tissues were weakly stained or negative.
Several cases of colorectal cancer, seminomal testis cancer, malignant lymphoma and glioma along with a few cases of breast and urothelial cancers displayed moderate cytoplasmic staining. Remaining cancer tissues were weakly stained or negative.
A majority of cancer tissues displayed weak to moderate cytoplasmic immunoreactivity.
GENE INFORMATIONi
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
HDAC6 (HGNC Symbol)
Synonyms
FLJ16239, HD6, JM21, KIAA0901, PPP1R90
Description
Histone deacetylase 6 (HGNC Symbol)
Entrez gene summary
Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene belongs to class II of the histone deacetylase/acuc/apha family. It contains an internal duplication of two catalytic domains which appear to function independently of each other. This protein possesses histone deacetylase activity and represses transcription. [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.
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 THUMBUP predicted membrane proteins Predicted intracellular proteins Disease related genes 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:0000209 [protein polyubiquitination] GO:0001047 [core promoter binding] GO:0003779 [actin binding] GO:0004407 [histone deacetylase activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005737 [cytoplasm] GO:0005771 [multivesicular body] GO:0005829 [cytosol] GO:0005874 [microtubule] GO:0005875 [microtubule associated complex] GO:0005881 [cytoplasmic microtubule] GO:0005901 [caveola] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006476 [protein deacetylation] GO:0006511 [ubiquitin-dependent protein catabolic process] GO:0006515 [misfolded or incompletely synthesized protein catabolic process] GO:0006886 [intracellular protein transport] GO:0006914 [autophagy] GO:0007026 [negative regulation of microtubule depolymerization] GO:0008013 [beta-catenin binding] GO:0008017 [microtubule binding] GO:0008270 [zinc ion binding] GO:0009636 [response to toxic substance] GO:0009967 [positive regulation of signal transduction] GO:0010033 [response to organic substance] GO:0010469 [regulation of receptor activity] GO:0010506 [regulation of autophagy] GO:0010634 [positive regulation of epithelial cell migration] GO:0010727 [negative regulation of hydrogen peroxide metabolic process] GO:0010870 [positive regulation of receptor biosynthetic process] GO:0016234 [inclusion body] GO:0016235 [aggresome] GO:0016241 [regulation of macroautophagy] GO:0016569 [covalent chromatin modification] GO:0016575 [histone deacetylation] GO:0016787 [hydrolase activity] GO:0019899 [enzyme binding] GO:0030286 [dynein complex] GO:0030424 [axon] GO:0030425 [dendrite] GO:0031252 [cell leading edge] GO:0031593 [polyubiquitin binding] GO:0031625 [ubiquitin protein ligase binding] GO:0031647 [regulation of protein stability] GO:0032041 [NAD-dependent histone deacetylase activity (H3-K14 specific)] GO:0032418 [lysosome localization] GO:0034983 [peptidyl-lysine deacetylation] GO:0035967 [cellular response to topologically incorrect protein] GO:0040029 [regulation of gene expression, epigenetic] GO:0042826 [histone deacetylase binding] GO:0042903 [tubulin deacetylase activity] GO:0042995 [cell projection] GO:0043005 [neuron projection] GO:0043014 [alpha-tubulin binding] GO:0043130 [ubiquitin binding] GO:0043162 [ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway] GO:0043204 [perikaryon] GO:0043234 [protein complex] GO:0043241 [protein complex disassembly] GO:0043242 [negative regulation of protein complex disassembly] GO:0044297 [cell body] GO:0045598 [regulation of fat cell differentiation] GO:0045861 [negative regulation of proteolysis] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0046872 [metal ion binding] GO:0048156 [tau protein binding] GO:0048471 [perinuclear region of cytoplasm] GO:0048487 [beta-tubulin binding] GO:0048668 [collateral sprouting] GO:0051354 [negative regulation of oxidoreductase activity] GO:0051646 [mitochondrion localization] GO:0051787 [misfolded protein binding] GO:0051788 [response to misfolded protein] GO:0051879 [Hsp90 protein binding] GO:0060271 [cilium assembly] GO:0060632 [regulation of microtubule-based movement] GO:0060765 [regulation of androgen receptor signaling pathway] GO:0060997 [dendritic spine morphogenesis] GO:0061734 [parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization] GO:0070201 [regulation of establishment of protein localization] GO:0070301 [cellular response to hydrogen peroxide] GO:0070840 [dynein complex binding] GO:0070842 [aggresome assembly] GO:0070845 [polyubiquitinated misfolded protein transport] GO:0070846 [Hsp90 deacetylation] GO:0070848 [response to growth factor] GO:0070932 [histone H3 deacetylation] GO:0071218 [cellular response to misfolded protein] GO:0090035 [positive regulation of chaperone-mediated protein complex assembly] GO:0090042 [tubulin deacetylation] GO:0098779 [positive regulation of macromitophagy in response to mitochondrial depolarization] GO:1901300 [positive regulation of hydrogen peroxide-mediated programmed cell death] GO:1903146 [regulation of mitophagy]
Enzymes ENZYME proteins Hydrolases THUMBUP predicted membrane proteins Predicted intracellular proteins Disease related genes FDA approved drug targets Small molecule drugs Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000118 [histone deacetylase complex] GO:0001047 [core promoter binding] GO:0003779 [actin binding] GO:0004407 [histone deacetylase activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005737 [cytoplasm] GO:0005771 [multivesicular body] GO:0005829 [cytosol] GO:0005874 [microtubule] GO:0005875 [microtubule associated complex] GO:0005901 [caveola] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006476 [protein deacetylation] GO:0006515 [misfolded or incompletely synthesized protein catabolic process] GO:0006886 [intracellular protein transport] GO:0006914 [autophagy] GO:0008013 [beta-catenin binding] GO:0008017 [microtubule binding] GO:0008270 [zinc ion binding] GO:0009636 [response to toxic substance] GO:0009967 [positive regulation of signal transduction] GO:0010033 [response to organic substance] GO:0010469 [regulation of receptor activity] GO:0010506 [regulation of autophagy] GO:0010634 [positive regulation of epithelial cell migration] GO:0010727 [negative regulation of hydrogen peroxide metabolic process] GO:0010870 [positive regulation of receptor biosynthetic process] GO:0016234 [inclusion body] GO:0016235 [aggresome] GO:0016241 [regulation of macroautophagy] GO:0016569 [covalent chromatin modification] GO:0016575 [histone deacetylation] GO:0016787 [hydrolase activity] GO:0019899 [enzyme binding] GO:0030286 [dynein complex] GO:0030424 [axon] GO:0030425 [dendrite] GO:0031252 [cell leading edge] GO:0031593 [polyubiquitin binding] GO:0031625 [ubiquitin protein ligase binding] GO:0031647 [regulation of protein stability] GO:0032041 [NAD-dependent histone deacetylase activity (H3-K14 specific)] GO:0032418 [lysosome localization] GO:0034983 [peptidyl-lysine deacetylation] GO:0035967 [cellular response to topologically incorrect protein] GO:0040029 [regulation of gene expression, epigenetic] GO:0042826 [histone deacetylase binding] GO:0042903 [tubulin deacetylase activity] GO:0042995 [cell projection] GO:0043014 [alpha-tubulin binding] GO:0043204 [perikaryon] GO:0043242 [negative regulation of protein complex disassembly] GO:0045861 [negative regulation of proteolysis] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0046872 [metal ion binding] GO:0048156 [tau protein binding] GO:0048471 [perinuclear region of cytoplasm] GO:0051354 [negative regulation of oxidoreductase activity] GO:0051787 [misfolded protein binding] GO:0051788 [response to misfolded protein] GO:0051879 [Hsp90 protein binding] GO:0060271 [cilium assembly] GO:0060632 [regulation of microtubule-based movement] GO:0060765 [regulation of androgen receptor signaling pathway] GO:0061734 [parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization] GO:0070301 [cellular response to hydrogen peroxide] GO:0070840 [dynein complex binding] GO:0070842 [aggresome assembly] GO:0070845 [polyubiquitinated misfolded protein transport] GO:0070846 [Hsp90 deacetylation] GO:0070848 [response to growth factor] GO:0070932 [histone H3 deacetylation] GO:0090035 [positive regulation of chaperone-mediated protein complex assembly] GO:0090042 [tubulin deacetylation] GO:1901300 [positive regulation of hydrogen peroxide-mediated programmed cell death] GO:1903146 [regulation of mitophagy]
The Human Protein Atlas project is funded
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