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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):
Mixed
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 and membranous expression in most tissues.
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 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.
A majority of cancer tissues displayed weak to moderate cytoplasmic positivity. Several colorectal and thyroid cancers along with a few endometrial cancers were strongly stained. Most cases of gliomas, lymphomas, melanomas, hepatocellular carcinomas and renal cancers were negative.
Cancer tissues showed weak to moderate cytoplasmic with additional membranous staining in several cases. A few cases of seminomas, malignant gliomas, lymphomas, colorectal and pancreatic cancers displayed strong positivity.
Cancer tissues displayed weak to moderate cytoplasmic staining. Most cases of lung, testicular, renal, stomach, pancreatic and liver cancers were negative.
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
BCR (HGNC Symbol)
Synonyms
ALL, BCR1, CML, D22S11, D22S662, PHL
Description
BCR, RhoGEF and GTPase activating protein (HGNC Symbol)
Entrez gene summary
A reciprocal translocation between chromosomes 22 and 9 produces the Philadelphia chromosome, which is often found in patients with chronic myelogenous leukemia. The chromosome 22 breakpoint for this translocation is located within the BCR gene. The translocation produces a fusion protein which is encoded by sequence from both BCR and ABL, the gene at the chromosome 9 breakpoint. Although the BCR-ABL fusion protein has been extensively studied, the function of the normal BCR gene product is not clear. The protein has serine/threonine kinase activity and is a GTPase-activating protein for p21rac. Two transcript variants encoding different isoforms have been found for this gene. [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.
BCR-001
BCR-002
BCR-006
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.
P11274 [Direct mapping] Breakpoint cluster region protein
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Enzymes ENZYME proteins Transferases Phobius predicted membrane proteins Predicted intracellular proteins Cancer-related genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Translocations Disease related genes FDA approved drug targets Small molecule drugs Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
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GO:0000166 [nucleotide binding] GO:0002692 [negative regulation of cellular extravasation] GO:0003014 [renal system process] GO:0004674 [protein serine/threonine kinase activity] GO:0004713 [protein tyrosine kinase activity] GO:0005085 [guanyl-nucleotide exchange factor activity] GO:0005089 [Rho guanyl-nucleotide exchange factor activity] GO:0005096 [GTPase activator activity] GO:0005515 [protein binding] GO:0005524 [ATP binding] GO:0005737 [cytoplasm] GO:0005829 [cytosol] GO:0005886 [plasma membrane] GO:0006468 [protein phosphorylation] GO:0007165 [signal transduction] GO:0007420 [brain development] GO:0014069 [postsynaptic density] GO:0016020 [membrane] GO:0016301 [kinase activity] GO:0016310 [phosphorylation] GO:0016740 [transferase activity] GO:0018108 [peptidyl-tyrosine phosphorylation] GO:0019899 [enzyme binding] GO:0030036 [actin cytoskeleton organization] GO:0030054 [cell junction] GO:0030336 [negative regulation of cell migration] GO:0032496 [response to lipopolysaccharide] GO:0035023 [regulation of Rho protein signal transduction] GO:0035556 [intracellular signal transduction] GO:0042472 [inner ear morphogenesis] GO:0043114 [regulation of vascular permeability] GO:0043234 [protein complex] GO:0043314 [negative regulation of neutrophil degranulation] GO:0043547 [positive regulation of GTPase activity] GO:0045202 [synapse] GO:0045211 [postsynaptic membrane] GO:0046777 [protein autophosphorylation] GO:0048008 [platelet-derived growth factor receptor signaling pathway] GO:0048872 [homeostasis of number of cells] GO:0050728 [negative regulation of inflammatory response] GO:0050766 [positive regulation of phagocytosis] GO:0050885 [neuromuscular process controlling balance] GO:0051056 [regulation of small GTPase mediated signal transduction] GO:0051171 [regulation of nitrogen compound metabolic process] GO:0051726 [regulation of cell cycle] GO:0060216 [definitive hemopoiesis] GO:0060268 [negative regulation of respiratory burst] GO:0060313 [negative regulation of blood vessel remodeling] GO:0065002 [intracellular protein transmembrane transport] GO:0070062 [extracellular exosome] GO:0071222 [cellular response to lipopolysaccharide] GO:2000378 [negative regulation of reactive oxygen species metabolic process]
P11274 [Direct mapping] Breakpoint cluster region protein
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Enzymes ENZYME proteins Transferases Phobius predicted membrane proteins Predicted intracellular proteins Cancer-related genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Translocations Disease related genes FDA approved drug targets Small molecule drugs Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
H0Y554 [Direct mapping] Breakpoint cluster region protein
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Predicted intracellular 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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GO:0005085 [guanyl-nucleotide exchange factor activity] GO:0005089 [Rho guanyl-nucleotide exchange factor activity] GO:0005622 [intracellular] GO:0035023 [regulation of Rho protein signal transduction] GO:0035556 [intracellular signal transduction] GO:0043547 [positive regulation of GTPase activity]
The Human Protein Atlas project is funded
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