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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):
Mixed
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.
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 cells displayed strong nuclear staining, in some cases accentuated to the nuclear membrane.
Nuclear and cytoplasmic staining in all cancer tissues, strongest staining in skin, urothelial and liver cancers.
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
RXRA (HGNC Symbol)
Synonyms
NR2B1
Description
Retinoid X receptor alpha (HGNC Symbol)
Entrez gene summary
Retinoid X receptors (RXRs) and retinoic acid receptors (RARs) are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors function as transcription factors by binding as homodimers or heterodimers to specific sequences in the promoters of target genes. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]
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.
RXRA-002
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.
Nuclear receptors Predicted intracellular proteins Transcription factors Zinc-coordinating DNA-binding domains Cancer-related genes Candidate cancer biomarkers Mutated cancer genes Mutational cancer driver genes FDA approved drug targets Small molecule drugs Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000790 [nuclear chromatin] GO:0000977 [RNA polymerase II regulatory region sequence-specific DNA binding] GO:0001701 [in utero embryonic development] GO:0001890 [placenta development] GO:0001893 [maternal placenta development] GO:0003677 [DNA binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0003707 [steroid hormone receptor activity] GO:0003708 [retinoic acid receptor activity] GO:0003713 [transcription coactivator activity] GO:0004879 [RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding] GO:0004886 [9-cis retinoic acid receptor activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006357 [regulation of transcription from RNA polymerase II promoter] GO:0006367 [transcription initiation from RNA polymerase II promoter] GO:0006766 [vitamin metabolic process] GO:0007507 [heart development] GO:0007566 [embryo implantation] GO:0008134 [transcription factor binding] GO:0008203 [cholesterol metabolic process] GO:0008270 [zinc ion binding] GO:0015721 [bile acid and bile salt transport] GO:0016032 [viral process] GO:0019048 [modulation by virus of host morphology or physiology] GO:0019899 [enzyme binding] GO:0031490 [chromatin DNA binding] GO:0032526 [response to retinoic acid] GO:0035357 [peroxisome proliferator activated receptor signaling pathway] GO:0042809 [vitamin D receptor binding] GO:0043010 [camera-type eye development] GO:0043235 [receptor complex] GO:0043401 [steroid hormone mediated signaling pathway] GO:0043565 [sequence-specific DNA binding] GO:0044212 [transcription regulatory region DNA binding] GO:0044255 [cellular lipid metabolic process] GO:0044323 [retinoic acid-responsive element binding] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0045994 [positive regulation of translational initiation by iron] GO:0046872 [metal ion binding] GO:0046982 [protein heterodimerization activity] GO:0048384 [retinoic acid receptor signaling pathway] GO:0051289 [protein homotetramerization] GO:0055010 [ventricular cardiac muscle tissue morphogenesis] GO:0055012 [ventricular cardiac muscle cell differentiation] GO:0060038 [cardiac muscle cell proliferation] GO:0060528 [secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development] GO:0060687 [regulation of branching involved in prostate gland morphogenesis] GO:0070644 [vitamin D response element binding] GO:0090575 [RNA polymerase II transcription factor complex] GO:1901522 [positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus]
The Human Protein Atlas project is funded
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