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 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.
Mainly cytoplasmic expression in most tissue types, including immune cells.
ANTIBODY IHC 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 (score description), divided into Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between the staining pattern of one antibody or several antibodies with RNA-seq data and available gene/protein characterization data.
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.
Gene product is not prognostic.
RNA EXPRESSION OVERVIEWi
RNA expression overview shows RNA-seq data from The Cancer Genome Atlas (TCGA).
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.
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, the fraction of samples with protein expression level high, medium, low, or not detected are provided by the blue-scale color-coding (as described by the color-coding scale in the box to the left). The length of the bar represents the number of patient samples analyzed (max=12 patients). 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. The mouse-over function displays additional data for the features in the staining summary view.
Next to the cancer staining data, the protein expression data of normal tissues or specific cell types corresponding to each cancer are shown and protein expression levels are indicated by the blue-scale color coding.
A manually written summary of the overall protein expression pattern across the analyzed cancer tissues.
Cancer tissues showed a variable staining pattern, mainly with weak to moderate cytoplasmic immunoreactivity. Strong positivity was observed in a few cases of ovarian-, prostate-, thyroid- and renal cancer.
This gene encodes a lymphokine involved in cell-mediated immunity, immunoregulation, and inflammation. It plays a role in the regulation of macrophage function in host defense through the suppression of anti-inflammatory effects of glucocorticoids. This lymphokine and the JAB1 protein form a complex in the cytosol near the peripheral plasma membrane, which may indicate an additional role in integrin signaling pathways. [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) (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 Isomerase Predicted intracellular proteins Plasma proteins Cancer-related genes Candidate cancer biomarkers Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
GO:0001516 [prostaglandin biosynthetic process] GO:0001934 [positive regulation of protein phosphorylation] GO:0002906 [negative regulation of mature B cell apoptotic process] GO:0004167 [dopachrome isomerase activity] GO:0005102 [receptor binding] GO:0005125 [cytokine activity] GO:0005126 [cytokine receptor binding] GO:0005515 [protein binding] GO:0005576 [extracellular region] GO:0005615 [extracellular space] GO:0005654 [nucleoplasm] GO:0005737 [cytoplasm] GO:0006954 [inflammatory response] GO:0007166 [cell surface receptor signaling pathway] GO:0007569 [cell aging] GO:0008283 [cell proliferation] GO:0009986 [cell surface] GO:0010629 [negative regulation of gene expression] GO:0010739 [positive regulation of protein kinase A signaling] GO:0019752 [carboxylic acid metabolic process] GO:0030330 [DNA damage response, signal transduction by p53 class mediator] GO:0030890 [positive regulation of B cell proliferation] GO:0031666 [positive regulation of lipopolysaccharide-mediated signaling pathway] GO:0031982 [vesicle] GO:0032269 [negative regulation of cellular protein metabolic process] GO:0033033 [negative regulation of myeloid cell apoptotic process] GO:0033138 [positive regulation of peptidyl-serine phosphorylation] GO:0042056 [chemoattractant activity] GO:0042127 [regulation of cell proliferation] GO:0042327 [positive regulation of phosphorylation] GO:0043030 [regulation of macrophage activation] GO:0043066 [negative regulation of apoptotic process] GO:0043209 [myelin sheath] GO:0043406 [positive regulation of MAP kinase activity] GO:0043518 [negative regulation of DNA damage response, signal transduction by p53 class mediator] GO:0045087 [innate immune response] GO:0048146 [positive regulation of fibroblast proliferation] GO:0050178 [phenylpyruvate tautomerase activity] GO:0050715 [positive regulation of cytokine secretion] GO:0050731 [positive regulation of peptidyl-tyrosine phosphorylation] GO:0050918 [positive chemotaxis] GO:0061078 [positive regulation of prostaglandin secretion involved in immune response] GO:0061081 [positive regulation of myeloid leukocyte cytokine production involved in immune response] GO:0070062 [extracellular exosome] GO:0070207 [protein homotrimerization] GO:0070374 [positive regulation of ERK1 and ERK2 cascade] GO:0071157 [negative regulation of cell cycle arrest] GO:0090238 [positive regulation of arachidonic acid secretion] GO:0090344 [negative regulation of cell aging] GO:1902166 [negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator] GO:2000343 [positive regulation of chemokine (C-X-C motif) ligand 2 production]