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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 (HUVEC TERT2)
HPA (normal tissue):
Expressed in all
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 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 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 cancers showed weak cytoplasmic staining. Strong nuclear staining was observed in gliomas. Several cancers showed vascular staining.
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
SMAD1 (HGNC Symbol)
Synonyms
JV4-1, MADH1, MADR1
Description
SMAD family member 1 (HGNC Symbol)
Entrez gene summary
The protein encoded by this gene belongs to the SMAD, a family of proteins similar to the gene products of the Drosophila gene 'mothers against decapentaplegic' (Mad) and the C. elegans gene Sma. SMAD proteins are signal transducers and transcriptional modulators that mediate multiple signaling pathways. This protein mediates the signals of the bone morphogenetic proteins (BMPs), which are involved in a range of biological activities including cell growth, apoptosis, morphogenesis, development and immune responses. In response to BMP ligands, this protein can be phosphorylated and activated by the BMP receptor kinase. The phosphorylated form of this protein forms a complex with SMAD4, which is important for its function in the transcription regulation. This protein is a target for SMAD-specific E3 ubiquitin ligases, such as SMURF1 and SMURF2, and undergoes ubiquitination and proteasome-mediated degradation. Alternatively spliced transcript variants encoding the same protein have been observed. [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.
SMAD1-001
SMAD1-002
SMAD1-003
SMAD1-004
SMAD1-005
SMAD1-006
SMAD1-007
SMAD1-012
SMAD1-015
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.
Q15797 [Direct mapping] Mothers against decapentaplegic homolog 1
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Predicted intracellular proteins Transcription factors beta-Hairpin exposed by an alpha/beta-scaffold Cancer-related genes Candidate cancer biomarkers Disease related genes Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
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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:0003677 [DNA binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0005057 [signal transducer activity, downstream of receptor] GO:0005515 [protein binding] GO:0005622 [intracellular] GO:0005634 [nucleus] GO:0005637 [nuclear inner membrane] GO:0005654 [nucleoplasm] GO:0005667 [transcription factor complex] GO:0005737 [cytoplasm] GO:0005829 [cytosol] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006366 [transcription from RNA polymerase II promoter] GO:0007165 [signal transduction] GO:0007179 [transforming growth factor beta receptor signaling pathway] GO:0007183 [SMAD protein complex assembly] GO:0009880 [embryonic pattern specification] GO:0010628 [positive regulation of gene expression] GO:0016021 [integral component of membrane] GO:0016579 [protein deubiquitination] GO:0019901 [protein kinase binding] GO:0030509 [BMP signaling pathway] GO:0030618 [transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity] GO:0031053 [primary miRNA processing] GO:0042802 [identical protein binding] GO:0043234 [protein complex] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0046872 [metal ion binding] GO:0060395 [SMAD protein signal transduction] GO:0070410 [co-SMAD binding] GO:0070411 [I-SMAD binding] GO:0071141 [SMAD protein complex] GO:1901522 [positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus]
Q15797 [Direct mapping] Mothers against decapentaplegic homolog 1
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Predicted intracellular proteins Transcription factors beta-Hairpin exposed by an alpha/beta-scaffold Cancer-related genes Candidate cancer biomarkers Disease related genes Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000165 [MAPK cascade] GO:0000978 [RNA polymerase II core promoter proximal region sequence-specific DNA binding] GO:0000979 [RNA polymerase II core promoter sequence-specific DNA binding] GO:0001077 [transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding] GO:0001657 [ureteric bud development] GO:0001710 [mesodermal cell fate commitment] GO:0002051 [osteoblast fate commitment] GO:0003677 [DNA binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0005057 [signal transducer activity, downstream of receptor] GO:0005515 [protein binding] GO:0005622 [intracellular] GO:0005634 [nucleus] GO:0005637 [nuclear inner membrane] GO:0005654 [nucleoplasm] GO:0005667 [transcription factor complex] GO:0005737 [cytoplasm] 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:0006468 [protein phosphorylation] GO:0006954 [inflammatory response] GO:0007165 [signal transduction] GO:0007179 [transforming growth factor beta receptor signaling pathway] GO:0007183 [SMAD protein complex assembly] GO:0007276 [gamete generation] GO:0008285 [negative regulation of cell proliferation] GO:0009880 [embryonic pattern specification] GO:0010628 [positive regulation of gene expression] GO:0016021 [integral component of membrane] GO:0016579 [protein deubiquitination] GO:0019901 [protein kinase binding] GO:0030509 [BMP signaling pathway] GO:0030618 [transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity] GO:0030901 [midbrain development] GO:0030902 [hindbrain development] GO:0031053 [primary miRNA processing] GO:0042592 [homeostatic process] GO:0042802 [identical protein binding] GO:0042803 [protein homodimerization activity] GO:0043234 [protein complex] GO:0045669 [positive regulation of osteoblast differentiation] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0046872 [metal ion binding] GO:0046982 [protein heterodimerization activity] GO:0051216 [cartilage development] GO:0060038 [cardiac muscle cell proliferation] GO:0060348 [bone development] GO:0060395 [SMAD protein signal transduction] GO:0061036 [positive regulation of cartilage development] GO:0070410 [co-SMAD binding] GO:0070411 [I-SMAD binding] GO:0070878 [primary miRNA binding] GO:0071141 [SMAD protein complex] GO:0071407 [cellular response to organic cyclic compound] 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:1902895 [positive regulation of pri-miRNA transcription from RNA polymerase II promoter]
Q15797 [Direct mapping] Mothers against decapentaplegic homolog 1
Show all
Predicted intracellular proteins Transcription factors beta-Hairpin exposed by an alpha/beta-scaffold Cancer-related genes Candidate cancer biomarkers Disease related genes Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
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:0003677 [DNA binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0005057 [signal transducer activity, downstream of receptor] GO:0005515 [protein binding] GO:0005622 [intracellular] GO:0005634 [nucleus] GO:0005637 [nuclear inner membrane] GO:0005654 [nucleoplasm] GO:0005667 [transcription factor complex] GO:0005737 [cytoplasm] GO:0005829 [cytosol] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006366 [transcription from RNA polymerase II promoter] GO:0007165 [signal transduction] GO:0007179 [transforming growth factor beta receptor signaling pathway] GO:0007183 [SMAD protein complex assembly] GO:0009880 [embryonic pattern specification] GO:0010628 [positive regulation of gene expression] GO:0016021 [integral component of membrane] GO:0016579 [protein deubiquitination] GO:0019901 [protein kinase binding] GO:0030509 [BMP signaling pathway] GO:0030618 [transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity] GO:0031053 [primary miRNA processing] GO:0042802 [identical protein binding] GO:0043234 [protein complex] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0046872 [metal ion binding] GO:0060395 [SMAD protein signal transduction] GO:0070410 [co-SMAD binding] GO:0070411 [I-SMAD binding] GO:0071141 [SMAD protein 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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