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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 (EFO-21, HUVEC TERT2, SK-BR-3, TIME)
HPA (normal tissue):
Tissue enhanced (placenta)
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.
Malignant cells showed moderate cytoplasmic immunoreactivity. Strong positivity was observed in prostate cancers. Most malignant lymphomas were weakly stained or negative.
Malignant cells generally showed weak to moderate cytoplasmic immunoreactivity. A few cases of malignant lymphomas showed strong cytoplasmic staining while a few liver cancer showed strong membranous positivity. Malignant gliomas were mainly negative.
Most malignant cells showed weak to moderate cytoplasmic and additional nuclear positivity. Several cases of malignant melanomas and ovarian carcinomas displayed strong staining. Malignant lymphomas and malignant gliomas were weakly stained or negative in most cases.
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
PDGFB (HGNC Symbol)
Synonyms
SIS, SSV
Description
Platelet derived growth factor subunit B (HGNC Symbol)
Entrez gene summary
This gene encodes a member of the protein family comprised of both platelet-derived growth factors (PDGF) and vascular endothelial growth factors (VEGF). The encoded preproprotein is proteolytically processed to generate platelet-derived growth factor subunit B, which can homodimerize, or alternatively, heterodimerize with the related platelet-derived growth factor subunit A. These proteins bind and activate PDGF receptor tyrosine kinases, which play a role in a wide range of developmental processes. Mutations in this gene are associated with meningioma. Reciprocal translocations between chromosomes 22 and 17, at sites where this gene and that for collagen type 1, alpha 1 are located, are associated with dermatofibrosarcoma protuberans, a rare skin tumor. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]
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.
PDGFB-001
PDGFB-002
PDGFB-003
PDGFB-004
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.
P01127 [Direct mapping] Platelet-derived growth factor subunit B
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Predicted intracellular proteins Plasma proteins RAS pathway related proteins Cancer-related genes Candidate cancer biomarkers COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Translocations Candidate cardiovascular disease genes Disease related genes Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
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GO:0000139 [Golgi membrane] GO:0000165 [MAPK cascade] GO:0001892 [embryonic placenta development] GO:0001938 [positive regulation of endothelial cell proliferation] GO:0002548 [monocyte chemotaxis] GO:0002576 [platelet degranulation] GO:0003104 [positive regulation of glomerular filtration] GO:0005088 [Ras guanyl-nucleotide exchange factor activity] GO:0005161 [platelet-derived growth factor receptor binding] GO:0005515 [protein binding] GO:0005518 [collagen binding] GO:0005576 [extracellular region] GO:0005615 [extracellular space] GO:0005737 [cytoplasm] GO:0005788 [endoplasmic reticulum lumen] GO:0005796 [Golgi lumen] GO:0006468 [protein phosphorylation] GO:0007179 [transforming growth factor beta receptor signaling pathway] GO:0007275 [multicellular organism development] GO:0007507 [heart development] GO:0008083 [growth factor activity] GO:0008284 [positive regulation of cell proliferation] GO:0009611 [response to wounding] GO:0009986 [cell surface] GO:0010512 [negative regulation of phosphatidylinositol biosynthetic process] GO:0010544 [negative regulation of platelet activation] GO:0010628 [positive regulation of gene expression] GO:0010629 [negative regulation of gene expression] GO:0014066 [regulation of phosphatidylinositol 3-kinase signaling] GO:0014068 [positive regulation of phosphatidylinositol 3-kinase signaling] GO:0014911 [positive regulation of smooth muscle cell migration] GO:0016020 [membrane] GO:0016176 [superoxide-generating NADPH oxidase activator activity] GO:0016323 [basolateral plasma membrane] GO:0018105 [peptidyl-serine phosphorylation] GO:0018108 [peptidyl-tyrosine phosphorylation] GO:0030198 [extracellular matrix organization] GO:0030335 [positive regulation of cell migration] GO:0031012 [extracellular matrix] GO:0031093 [platelet alpha granule lumen] GO:0031954 [positive regulation of protein autophosphorylation] GO:0032091 [negative regulation of protein binding] GO:0032147 [activation of protein kinase activity] GO:0032148 [activation of protein kinase B activity] GO:0035655 [interleukin-18-mediated signaling pathway] GO:0035793 [positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway] GO:0038001 [paracrine signaling] GO:0042056 [chemoattractant activity] GO:0042802 [identical protein binding] GO:0042803 [protein homodimerization activity] GO:0043406 [positive regulation of MAP kinase activity] GO:0043410 [positive regulation of MAPK cascade] GO:0043536 [positive regulation of blood vessel endothelial cell migration] GO:0043547 [positive regulation of GTPase activity] GO:0043552 [positive regulation of phosphatidylinositol 3-kinase activity] GO:0045737 [positive regulation of cyclin-dependent protein serine/threonine kinase activity] GO:0045740 [positive regulation of DNA replication] GO:0045840 [positive regulation of mitotic nuclear division] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0046854 [phosphatidylinositol phosphorylation] GO:0046934 [phosphatidylinositol-4,5-bisphosphate 3-kinase activity] GO:0046982 [protein heterodimerization activity] GO:0048008 [platelet-derived growth factor receptor signaling pathway] GO:0048015 [phosphatidylinositol-mediated signaling] GO:0048146 [positive regulation of fibroblast proliferation] GO:0048407 [platelet-derived growth factor binding] GO:0048661 [positive regulation of smooth muscle cell proliferation] GO:0050731 [positive regulation of peptidyl-tyrosine phosphorylation] GO:0050918 [positive chemotaxis] GO:0050921 [positive regulation of chemotaxis] GO:0051781 [positive regulation of cell division] GO:0060326 [cell chemotaxis] GO:0061098 [positive regulation of protein tyrosine kinase activity] GO:0070374 [positive regulation of ERK1 and ERK2 cascade] GO:0070528 [protein kinase C signaling] GO:0071363 [cellular response to growth factor stimulus] GO:0071506 [cellular response to mycophenolic acid] GO:0072126 [positive regulation of glomerular mesangial cell proliferation] GO:0072255 [metanephric glomerular mesangial cell development] GO:0072593 [reactive oxygen species metabolic process] GO:0090280 [positive regulation of calcium ion import] GO:1900127 [positive regulation of hyaluronan biosynthetic process] GO:1902894 [negative regulation of pri-miRNA transcription from RNA polymerase II promoter] GO:1902895 [positive regulation of pri-miRNA transcription from RNA polymerase II promoter] GO:1904707 [positive regulation of vascular smooth muscle cell proliferation] GO:1904754 [positive regulation of vascular associated smooth muscle cell migration] GO:1905064 [negative regulation of vascular smooth muscle cell differentiation] GO:1905176 [positive regulation of vascular smooth muscle cell dedifferentiation] GO:2000379 [positive regulation of reactive oxygen species metabolic process] GO:2000573 [positive regulation of DNA biosynthetic process] GO:2000587 [negative regulation of platelet-derived growth factor receptor-beta signaling pathway] GO:2000591 [positive regulation of metanephric mesenchymal cell migration]
A9UJP0 [Direct mapping] Platelet-derived growth factor subunit B
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Predicted intracellular proteins RAS pathway related proteins Cancer-related genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Translocations Protein evidence (Ezkurdia et al 2014)
A9UJN9 [Direct mapping] Platelet-derived growth factor subunit B
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Predicted intracellular proteins RAS pathway related proteins Cancer-related genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Translocations Protein evidence (Ezkurdia et al 2014)
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