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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):
Mixed
HPA (cell line):
Cell line enhanced (AF22, WM-115)
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.
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 - 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.
Gene product is not prognostic.
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RNA EXPRESSION OVERVIEWi
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.
Most cancer cells displayed weak to moderate nuclear staining, often only in a few cells. A few cervical cancers, breast cancers and melanomas were strongly 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
GLI3 (HGNC Symbol)
Synonyms
ACLS, GCPS, PAP-A, PAPA, PAPA1, PAPB, PHS, PPDIV
Description
GLI family zinc finger 3 (HGNC Symbol)
Entrez gene summary
This gene encodes a protein which belongs to the C2H2-type zinc finger proteins subclass of the Gli family. They are characterized as DNA-binding transcription factors and are mediators of Sonic hedgehog (Shh) signaling. The protein encoded by this gene localizes in the cytoplasm and activates patched Drosophila homolog (PTCH) gene expression. It is also thought to play a role during embryogenesis. Mutations in this gene have been associated with several diseases, including Greig cephalopolysyndactyly syndrome, Pallister-Hall syndrome, preaxial polydactyly type IV, and postaxial polydactyly types A1 and B. [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.
GLI3-001
GLI3-004
GLI3-005
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.
Predicted intracellular proteins Transcription factors Zinc-coordinating DNA-binding domains Disease related genes Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
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GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000977 [RNA polymerase II regulatory region sequence-specific DNA binding] GO:0000978 [RNA polymerase II core promoter proximal region sequence-specific DNA binding] GO:0001077 [transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding] GO:0001656 [metanephros development] GO:0001658 [branching involved in ureteric bud morphogenesis] GO:0001701 [in utero embryonic development] GO:0001822 [kidney development] GO:0002052 [positive regulation of neuroblast proliferation] GO:0003676 [nucleic acid binding] GO:0003677 [DNA binding] GO:0003682 [chromatin binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005737 [cytoplasm] GO:0005829 [cytosol] GO:0005929 [cilium] GO:0005930 [axoneme] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006366 [transcription from RNA polymerase II promoter] GO:0007224 [smoothened signaling pathway] GO:0007389 [pattern specification process] GO:0007411 [axon guidance] GO:0007417 [central nervous system development] GO:0007420 [brain development] GO:0007442 [hindgut morphogenesis] GO:0007507 [heart development] GO:0008013 [beta-catenin binding] GO:0008285 [negative regulation of cell proliferation] GO:0009952 [anterior/posterior pattern specification] GO:0009953 [dorsal/ventral pattern formation] GO:0009954 [proximal/distal pattern formation] GO:0010468 [regulation of gene expression] GO:0016485 [protein processing] GO:0016592 [mediator complex] GO:0016607 [nuclear speck] GO:0017053 [transcriptional repressor complex] GO:0021513 [spinal cord dorsal/ventral patterning] GO:0021522 [spinal cord motor neuron differentiation] GO:0021537 [telencephalon development] GO:0021543 [pallium development] GO:0021544 [subpallium development] GO:0021631 [optic nerve morphogenesis] GO:0021766 [hippocampus development] GO:0021775 [smoothened signaling pathway involved in ventral spinal cord interneuron specification] GO:0021776 [smoothened signaling pathway involved in spinal cord motor neuron cell fate specification] GO:0021798 [forebrain dorsal/ventral pattern formation] GO:0021801 [cerebral cortex radial glia guided migration] GO:0021819 [layer formation in cerebral cortex] GO:0021861 [forebrain radial glial cell differentiation] GO:0021915 [neural tube development] GO:0022018 [lateral ganglionic eminence cell proliferation] GO:0030318 [melanocyte differentiation] GO:0030324 [lung development] GO:0030326 [embryonic limb morphogenesis] GO:0030879 [mammary gland development] GO:0030900 [forebrain development] GO:0032332 [positive regulation of chondrocyte differentiation] GO:0033077 [T cell differentiation in thymus] GO:0035035 [histone acetyltransferase binding] GO:0035108 [limb morphogenesis] GO:0035295 [tube development] GO:0042060 [wound healing] GO:0042127 [regulation of cell proliferation] GO:0042307 [positive regulation of protein import into nucleus] GO:0042475 [odontogenesis of dentin-containing tooth] GO:0042733 [embryonic digit morphogenesis] GO:0042826 [histone deacetylase binding] GO:0042981 [regulation of apoptotic process] GO:0042995 [cell projection] GO:0043010 [camera-type eye development] GO:0043066 [negative regulation of apoptotic process] GO:0043565 [sequence-specific DNA binding] GO:0043585 [nose morphogenesis] GO:0043586 [tongue development] GO:0043627 [response to estrogen] GO:0045060 [negative thymic T cell selection] GO:0045595 [regulation of cell differentiation] GO:0045596 [negative regulation of cell differentiation] GO:0045665 [negative regulation of neuron differentiation] GO:0045669 [positive regulation of osteoblast differentiation] GO:0045879 [negative regulation of smoothened signaling pathway] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0046638 [positive regulation of alpha-beta T cell differentiation] GO:0046639 [negative regulation of alpha-beta T cell differentiation] GO:0046872 [metal ion binding] GO:0048557 [embryonic digestive tract morphogenesis] GO:0048566 [embryonic digestive tract development] GO:0048568 [embryonic organ development] GO:0048589 [developmental growth] GO:0048593 [camera-type eye morphogenesis] GO:0048598 [embryonic morphogenesis] GO:0048646 [anatomical structure formation involved in morphogenesis] GO:0048663 [neuron fate commitment] GO:0048704 [embryonic skeletal system morphogenesis] GO:0048709 [oligodendrocyte differentiation] GO:0048754 [branching morphogenesis of an epithelial tube] GO:0048839 [inner ear development] GO:0048856 [anatomical structure development] GO:0060021 [palate development] GO:0060173 [limb development] GO:0060364 [frontal suture morphogenesis] GO:0060366 [lambdoid suture morphogenesis] GO:0060367 [sagittal suture morphogenesis] GO:0060594 [mammary gland specification] GO:0060831 [smoothened signaling pathway involved in dorsal/ventral neural tube patterning] GO:0060840 [artery development] GO:0060873 [anterior semicircular canal development] GO:0060875 [lateral semicircular canal development] GO:0061005 [cell differentiation involved in kidney development] GO:0070242 [thymocyte apoptotic process] GO:0090090 [negative regulation of canonical Wnt signaling pathway] GO:0097542 [ciliary tip] GO:0097546 [ciliary base] GO:1903010 [regulation of bone development]