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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):
Cell line enhanced (Karpas-707, REH)
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.
Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.
Antibody staining mainly 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.
Cancer tissues generally displayed weak to moderate cytoplasmic positivity. Lymphoid cells and endothelial cells of tumor stroma were distinctly stained.
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
TNFAIP3 (HGNC Symbol)
Synonyms
A20, OTUD7C
Description
TNF alpha induced protein 3 (HGNC Symbol)
Entrez gene summary
This gene was identified as a gene whose expression is rapidly induced by the tumor necrosis factor (TNF). The protein encoded by this gene is a zinc finger protein and ubiqitin-editing enzyme, and has been shown to inhibit NF-kappa B activation as well as TNF-mediated apoptosis. The encoded protein, which has both ubiquitin ligase and deubiquitinase activities, is involved in the cytokine-mediated immune and inflammatory responses. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2012]
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.
TNFAIP3-001
TNFAIP3-002
TNFAIP3-003
TNFAIP3-004
TNFAIP3-201
TNFAIP3-202
TNFAIP3-203
TNFAIP3-204
TNFAIP3-205
TNFAIP3-206
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.
Q5VXR0 [Direct mapping] Tumor necrosis factor alpha-induced protein 3
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Predicted intracellular proteins Cancer-related genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Nonsense Mutations COSMIC Large Deletions COSMIC Frameshift Mutations Protein evidence (Ezkurdia et al 2014)
Q5VXQ8 [Direct mapping] Tumor necrosis factor alpha-induced protein 3
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Predicted intracellular proteins Cancer-related genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Nonsense Mutations COSMIC Large Deletions COSMIC Frameshift Mutations Protein evidence (Ezkurdia et al 2014)
Q5VXQ9 [Direct mapping] Tumor necrosis factor alpha-induced protein 3
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Predicted intracellular proteins Cancer-related genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Nonsense Mutations COSMIC Large Deletions COSMIC Frameshift Mutations Protein evidence (Ezkurdia et al 2014)
Enzymes ENZYME proteins Hydrolases Peptidases Cysteine-type peptidases Predicted intracellular proteins Plasma proteins Cancer-related genes Candidate cancer biomarkers COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Nonsense Mutations COSMIC Large Deletions COSMIC Frameshift Mutations Disease related genes Potential drug targets Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
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GO:0001922 [B-1 B cell homeostasis] GO:0002020 [protease binding] GO:0002237 [response to molecule of bacterial origin] GO:0002634 [regulation of germinal center formation] GO:0002677 [negative regulation of chronic inflammatory response] GO:0003677 [DNA binding] GO:0003824 [catalytic activity] GO:0004842 [ubiquitin-protein transferase activity] GO:0004843 [thiol-dependent ubiquitin-specific protease activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005737 [cytoplasm] GO:0005764 [lysosome] GO:0005829 [cytosol] GO:0006508 [proteolysis] GO:0006915 [apoptotic process] GO:0006954 [inflammatory response] GO:0008152 [metabolic process] GO:0008233 [peptidase activity] GO:0008234 [cysteine-type peptidase activity] GO:0008270 [zinc ion binding] GO:0010803 [regulation of tumor necrosis factor-mediated signaling pathway] GO:0016567 [protein ubiquitination] GO:0016579 [protein deubiquitination] GO:0016787 [hydrolase activity] GO:0016874 [ligase activity] GO:0019900 [kinase binding] GO:0031397 [negative regulation of protein ubiquitination] GO:0032088 [negative regulation of NF-kappaB transcription factor activity] GO:0032480 [negative regulation of type I interferon production] GO:0032495 [response to muramyl dipeptide] GO:0032691 [negative regulation of interleukin-1 beta production] GO:0032703 [negative regulation of interleukin-2 production] GO:0032715 [negative regulation of interleukin-6 production] GO:0032720 [negative regulation of tumor necrosis factor production] GO:0034136 [negative regulation of toll-like receptor 2 signaling pathway] GO:0034140 [negative regulation of toll-like receptor 3 signaling pathway] GO:0034144 [negative regulation of toll-like receptor 4 signaling pathway] GO:0034148 [negative regulation of toll-like receptor 5 signaling pathway] GO:0035871 [protein K11-linked deubiquitination] GO:0036459 [thiol-dependent ubiquitinyl hydrolase activity] GO:0042802 [identical protein binding] GO:0043124 [negative regulation of I-kappaB kinase/NF-kappaB signaling] GO:0043130 [ubiquitin binding] GO:0043621 [protein self-association] GO:0045732 [positive regulation of protein catabolic process] GO:0045736 [negative regulation of cyclin-dependent protein serine/threonine kinase activity] GO:0045779 [negative regulation of bone resorption] GO:0045824 [negative regulation of innate immune response] GO:0046872 [metal ion binding] GO:0048662 [negative regulation of smooth muscle cell proliferation] GO:0050691 [regulation of defense response to virus by host] GO:0050727 [regulation of inflammatory response] GO:0050728 [negative regulation of inflammatory response] GO:0050869 [negative regulation of B cell activation] GO:0051259 [protein oligomerization] GO:0060548 [negative regulation of cell death] GO:0061043 [regulation of vascular wound healing] GO:0061578 [Lys63-specific deubiquitinase activity] GO:0070062 [extracellular exosome] GO:0070301 [cellular response to hydrogen peroxide] GO:0070423 [nucleotide-binding oligomerization domain containing signaling pathway] GO:0070429 [negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway] GO:0070433 [negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway] GO:0070530 [K63-linked polyubiquitin binding] GO:0070536 [protein K63-linked deubiquitination] GO:0070936 [protein K48-linked ubiquitination] GO:0071108 [protein K48-linked deubiquitination] GO:0071222 [cellular response to lipopolysaccharide] GO:0071947 [protein deubiquitination involved in ubiquitin-dependent protein catabolic process] GO:0072573 [tolerance induction to lipopolysaccharide] GO:0072666 [establishment of protein localization to vacuole] GO:0090291 [negative regulation of osteoclast proliferation] GO:1902042 [negative regulation of extrinsic apoptotic signaling pathway via death domain receptors] GO:1903364 [positive regulation of cellular protein catabolic process] GO:2000347 [positive regulation of hepatocyte proliferation] GO:2000349 [negative regulation of CD40 signaling pathway] GO:2000352 [negative regulation of endothelial cell apoptotic process]
A0A087WXL5 [Direct mapping] Tumor necrosis factor alpha-induced protein 3
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Predicted intracellular proteins Cancer-related genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Nonsense Mutations COSMIC Large Deletions COSMIC Frameshift Mutations Protein evidence (Ezkurdia et al 2014)
A0A087WVN3 [Direct mapping] Tumor necrosis factor alpha-induced protein 3
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Predicted intracellular proteins Cancer-related genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Nonsense Mutations COSMIC Large Deletions COSMIC Frameshift Mutations Protein evidence (Ezkurdia et al 2014)
A0A087WU80 [Direct mapping] Tumor necrosis factor alpha-induced protein 3
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Predicted intracellular proteins Cancer-related genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Nonsense Mutations COSMIC Large Deletions COSMIC Frameshift Mutations Protein evidence (Ezkurdia et al 2014)
D3TTY5 [Direct mapping] Truncated tumor necrosis factor alpha-induced protein 3; Tumor necrosis factor alpha-induced protein 3
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Predicted intracellular proteins Cancer-related genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Nonsense Mutations COSMIC Large Deletions COSMIC Frameshift Mutations Protein evidence (Ezkurdia et al 2014)
A0A087X1N1 [Direct mapping] Tumor necrosis factor alpha-induced protein 3
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Predicted intracellular proteins Cancer-related genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Nonsense Mutations COSMIC Large Deletions COSMIC Frameshift Mutations Protein evidence (Ezkurdia et al 2014)
The Human Protein Atlas project is funded
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