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RNA category is based on mRNA expression levels in the analyzed samples (RNA assay description). The categories include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected. RNA category is calculated separately for data imported from The Genotype-Tissue Expression project (GTEX), FANTOM5 Consortium (FANTOM5) and internally generated Human Protein Atlas (HPA) data.
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 expressioni
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 nuclear 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 scorei
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.
Below is an overview of RNA and protein expression data generated in the Human Protein Atlas project. Analyzed tissues are divided into color-coded groups according to which functional features they have in common. For each group, a list of included tissues is accessed by clicking on group name, group symbol, RNA bar, or protein bar. Subsequent selection of a particular tissue in this list links to the image data page.
Images of selected tissues give a visual summary of the protein expression profile furthest to the right.
The gray human body provides links to a histology dictionary when clicking on any part of the figure.
RNA expression (TPM)i
RNA-seq results generated in HPA are reported as number of transcripts per million (TPM). Each bar represents the highest expression score found in a particular group of tissues. The assay is described more in detail in Assays & Annotation.
Protein expression (score)i
Each bar represents the highest expression score found in a particular group of tissues. Protein expression scores are based on a best estimate of the "true" protein expression from a knowledge-based annotation, described more in detail under Assays & annotation. For genes where more than one antibody has been used, a collective score is set displaying the estimated true protein expression.
Protein expression data is shown for each of the 44 tissues. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. Mouse-over function shows protein score for analyzed cell types in a selected tissue. To access image data click on tissue name or bar. Annotation of protein expression is described in detail in Assays & annotation.
For genes with available protein data for which a knowledge-based annotation gave inconclusive results, no protein expression data is displayed in the protein expression data overview. However, all immunohistochemical images are still available and the annotation data can be found under Primary data.
Organ
Expression
Alphabetical
RNA EXPRESSION OVERVIEWi
RNA expression overview shows RNA-data from three different sources: Internally generated Human Protein Atlas (HPA) RNA-seq data, RNA-seq data from the Genotype-Tissue Expression (GTEx) project and CAGE data from FANTOM5 project. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
HPA dataseti
HPA dataset RNA-seq tissue data is reported as mean TPM (transcripts per million), corresponding to mean values of the different individual samples from each tissue. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar. The RNA-seq assay is described in detail in Assays & Annotation.
RNA tissue category HPA HPA RNA tissue category (category description) is calculated based on mRNA expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all
GTEx dataseti
GTEx dataset RNA-seq data is reported as median RPKM (reads per kilobase per million mapped reads), generated by the Genotype-Tissue Expression (GTEx) project. More information can be found in Assays & Annotation.
RNA tissue category GTEx GTEx RNA tissue category (category description) is calculated based on mRNA expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all
FANTOM5 dataseti
FANTOM5 dataset Tissue data obtained through Cap Analysis of Gene Expression (CAGE) are reported as Tags Per Million, generated by the FANTOM5 project. More information can be found in Assays & Annotation.
RNA tissue category FANTOM5 FANTOM5 RNA tissue category (category description) is calculated based on gene expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all
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
SMAD4 (HGNC Symbol)
Synonyms
DPC4, MADH4
Description
SMAD family member 4 (HGNC Symbol)
Entrez gene summary
This gene encodes a member of the Smad family of signal transduction proteins. Smad proteins are phosphorylated and activated by transmembrane serine-threonine receptor kinases in response to TGF-beta signaling. The product of this gene forms homomeric complexes and heteromeric complexes with other activated Smad proteins, which then accumulate in the nucleus and regulate the transcription of target genes. This protein binds to DNA and recognizes an 8-bp palindromic sequence (GTCTAGAC) called the Smad-binding element (SBE). The Smad proteins are subject to complex regulation by post-translational modifications. Mutations or deletions in this gene have been shown to result in pancreatic cancer, juvenile polyposis syndrome, and hereditary hemorrhagic telangiectasia syndrome. [provided by RefSeq, Oct 2009]
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.
SMAD4-001
SMAD4-004
SMAD4-006
SMAD4-007
SMAD4-008
SMAD4-010
SMAD4-013
SMAD4-016
SMAD4-201
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.
Q13485 [Direct mapping] Mothers against decapentaplegic homolog 4 A0A024R274 [Target identity:100%; Query identity:100%] Mothers against decapentaplegic homolog
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SCAMPI predicted membrane proteins Predicted intracellular proteins Transcription factors beta-Hairpin exposed by an alpha/beta-scaffold Cancer-related genes Candidate cancer biomarkers Mutated cancer genes Mutational cancer driver genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Nonsense Mutations COSMIC Missense Mutations COSMIC Large Deletions COSMIC Germline Mutations COSMIC Frameshift Mutations Disease related genes Protein evidence (Ezkurdia et al 2014)
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GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000790 [nuclear chromatin] GO:0000978 [RNA polymerase II core promoter proximal region sequence-specific DNA binding] GO:0000987 [core promoter proximal region sequence-specific DNA binding] GO:0000988 [transcription factor activity, protein binding] GO:0001077 [transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding] GO:0001666 [response to hypoxia] GO:0003148 [outflow tract septum morphogenesis] GO:0003220 [left ventricular cardiac muscle tissue morphogenesis] GO:0003677 [DNA binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0005515 [protein binding] GO:0005622 [intracellular] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005667 [transcription factor complex] GO:0005737 [cytoplasm] GO:0005813 [centrosome] GO:0005829 [cytosol] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006366 [transcription from RNA polymerase II promoter] GO:0006879 [cellular iron ion homeostasis] GO:0007179 [transforming growth factor beta receptor signaling pathway] GO:0007183 [SMAD protein complex assembly] GO:0010614 [negative regulation of cardiac muscle hypertrophy] GO:0010718 [positive regulation of epithelial to mesenchymal transition] GO:0010862 [positive regulation of pathway-restricted SMAD protein phosphorylation] GO:0016579 [protein deubiquitination] GO:0017015 [regulation of transforming growth factor beta receptor signaling pathway] GO:0030308 [negative regulation of cell growth] GO:0030509 [BMP signaling pathway] GO:0030511 [positive regulation of transforming growth factor beta receptor signaling pathway] GO:0030513 [positive regulation of BMP signaling pathway] GO:0030616 [transforming growth factor beta receptor, common-partner cytoplasmic mediator activity] GO:0032444 [activin responsive factor complex] GO:0032909 [regulation of transforming growth factor beta2 production] GO:0035019 [somatic stem cell population maintenance] GO:0035556 [intracellular signal transduction] GO:0042802 [identical protein binding] GO:0042803 [protein homodimerization activity] GO:0043565 [sequence-specific DNA binding] GO:0044212 [transcription regulatory region DNA binding] 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:0046872 [metal ion binding] GO:0051571 [positive regulation of histone H3-K4 methylation] GO:0060021 [palate development] GO:0060391 [positive regulation of SMAD protein import into nucleus] GO:0060395 [SMAD protein signal transduction] GO:0060412 [ventricular septum morphogenesis] GO:0070102 [interleukin-6-mediated signaling pathway] GO:0070373 [negative regulation of ERK1 and ERK2 cascade] GO:0070411 [I-SMAD binding] GO:0070412 [R-SMAD binding] GO:0071141 [SMAD protein complex] GO:0071559 [response to transforming growth factor beta] GO:0071773 [cellular response to BMP stimulus] GO:1901522 [positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus] GO:1905305 [negative regulation of cardiac myofibril assembly] GO:2000617 [positive regulation of histone H3-K9 acetylation]
Q13485 [Direct mapping] Mothers against decapentaplegic homolog 4 A0A024R274 [Target identity:100%; Query identity:100%] Mothers against decapentaplegic homolog
Show all
SCAMPI predicted membrane proteins Predicted intracellular proteins Transcription factors beta-Hairpin exposed by an alpha/beta-scaffold Cancer-related genes Candidate cancer biomarkers Mutated cancer genes Mutational cancer driver genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Nonsense Mutations COSMIC Missense Mutations COSMIC Large Deletions COSMIC Germline Mutations COSMIC Frameshift Mutations 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:0000790 [nuclear chromatin] 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:0000987 [core promoter proximal region sequence-specific DNA binding] GO:0000988 [transcription factor activity, protein binding] GO:0001076 [transcription factor activity, RNA polymerase II transcription factor binding] GO:0001077 [transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding] GO:0001085 [RNA polymerase II transcription factor binding] GO:0001228 [transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding] GO:0001541 [ovarian follicle development] GO:0001658 [branching involved in ureteric bud morphogenesis] GO:0001666 [response to hypoxia] GO:0001701 [in utero embryonic development] GO:0001702 [gastrulation with mouth forming second] GO:0001822 [kidney development] GO:0003148 [outflow tract septum morphogenesis] GO:0003190 [atrioventricular valve formation] GO:0003198 [epithelial to mesenchymal transition involved in endocardial cushion formation] GO:0003220 [left ventricular cardiac muscle tissue morphogenesis] GO:0003251 [positive regulation of cell proliferation involved in heart valve morphogenesis] GO:0003279 [cardiac septum development] GO:0003360 [brainstem development] GO:0003677 [DNA binding] GO:0003682 [chromatin binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0005515 [protein binding] GO:0005518 [collagen binding] GO:0005622 [intracellular] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005667 [transcription factor complex] GO:0005737 [cytoplasm] GO:0005813 [centrosome] GO:0005829 [cytosol] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006357 [regulation of transcription from RNA polymerase II promoter] GO:0006366 [transcription from RNA polymerase II promoter] GO:0006879 [cellular iron ion homeostasis] GO:0007179 [transforming growth factor beta receptor signaling pathway] GO:0007183 [SMAD protein complex assembly] GO:0007283 [spermatogenesis] GO:0007338 [single fertilization] GO:0007369 [gastrulation] GO:0007411 [axon guidance] GO:0007492 [endoderm development] GO:0007498 [mesoderm development] GO:0008283 [cell proliferation] GO:0008285 [negative regulation of cell proliferation] GO:0008584 [male gonad development] GO:0008585 [female gonad development] GO:0009952 [anterior/posterior pattern specification] GO:0010614 [negative regulation of cardiac muscle hypertrophy] GO:0010718 [positive regulation of epithelial to mesenchymal transition] GO:0010862 [positive regulation of pathway-restricted SMAD protein phosphorylation] GO:0014033 [neural crest cell differentiation] GO:0016579 [protein deubiquitination] GO:0017015 [regulation of transforming growth factor beta receptor signaling pathway] GO:0030308 [negative regulation of cell growth] GO:0030509 [BMP signaling pathway] GO:0030511 [positive regulation of transforming growth factor beta receptor signaling pathway] GO:0030513 [positive regulation of BMP signaling pathway] GO:0030616 [transforming growth factor beta receptor, common-partner cytoplasmic mediator activity] GO:0032444 [activin responsive factor complex] GO:0032525 [somite rostral/caudal axis specification] GO:0032909 [regulation of transforming growth factor beta2 production] GO:0033686 [positive regulation of luteinizing hormone secretion] GO:0035019 [somatic stem cell population maintenance] GO:0035556 [intracellular signal transduction] GO:0036302 [atrioventricular canal development] GO:0042118 [endothelial cell activation] GO:0042127 [regulation of cell proliferation] GO:0042733 [embryonic digit morphogenesis] GO:0042802 [identical protein binding] GO:0042803 [protein homodimerization activity] GO:0043565 [sequence-specific DNA binding] GO:0044212 [transcription regulatory region DNA binding] 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:0046872 [metal ion binding] GO:0046881 [positive regulation of follicle-stimulating hormone secretion] GO:0046982 [protein heterodimerization activity] GO:0048589 [developmental growth] GO:0048663 [neuron fate commitment] GO:0048729 [tissue morphogenesis] GO:0048733 [sebaceous gland development] GO:0048859 [formation of anatomical boundary] GO:0051098 [regulation of binding] GO:0051571 [positive regulation of histone H3-K4 methylation] GO:0051797 [regulation of hair follicle development] GO:0060021 [palate development] GO:0060065 [uterus development] GO:0060391 [positive regulation of SMAD protein import into nucleus] GO:0060395 [SMAD protein signal transduction] GO:0060412 [ventricular septum morphogenesis] GO:0060548 [negative regulation of cell death] GO:0060956 [endocardial cell differentiation] GO:0061040 [female gonad morphogenesis] GO:0070102 [interleukin-6-mediated signaling pathway] GO:0070373 [negative regulation of ERK1 and ERK2 cascade] GO:0070411 [I-SMAD binding] GO:0070412 [R-SMAD binding] GO:0071141 [SMAD protein complex] GO:0071559 [response to transforming growth factor beta] GO:0071773 [cellular response to BMP stimulus] GO:0072133 [metanephric mesenchyme morphogenesis] GO:0072134 [nephrogenic mesenchyme morphogenesis] GO:0072520 [seminiferous tubule development] 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] GO:1905305 [negative regulation of cardiac myofibril assembly] GO:2000617 [positive regulation of histone H3-K9 acetylation]
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