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The RNA tissue category is based on mRNA expression levels in 32 different tissues (RNA assay description).
The categories include: tissue enriched, group enriched, tissue enhanced, expressed in all, not detected, and mixed.
RNA tissue category is calculated separately both for internally generated Human Protein Atlas (HPA) RNA-seq data, as
well as RNA-seq data from the Genotype-Tissue Expression (GTEx) consortium.
Protein evidence
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.
Protein localization
A summary of the overall protein expression pattern across the analyzed tissues. The summary is based on knowledge-based
annotation (Annotation description). For genes pending
knowledge-based annotation, the protein localization refers to the antibody staining pattern.
"RNA-based expert annotation gave inconconclusive results" 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.
RNA tissue category
HPA:
Expressed in all
GTEx:
Expressed in all
Protein evidence
Evidence at protein level
Protein localization
Cytoplasmic expression in many cell types with highest expression levels in placenta and gastrointestinal tract.
Standardized explanatory sentences with additional information required for full understanding of the
knowledge-based expression profile. Currently, not all genes have been analyzed by knowledge-based
annotation, indicated by "Pending RNA-based expert annotation", when applicable.
Data reliability
Data reliability score (score description), divided into supportive (premium)
or uncertain (not premium), is based on consistency between the staining pattern of one antibody or several
antibodies with RNA-seq data and available gene/protein characterization data.
Below to the right is an overview of RNA and protein expression data generated in the HPA project. Analyzed tissues are divided into 13 color-coded
groups according to common functional features. 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 below to the left. The gray human
body in the middle provides links to a histology dictionary when clicking on any part of the figure.
RNA expression (FPKM)
RNA–seq results generated in HPA are reported as number of Fragments Per Kilobase gene model and Million reads (FPKM).
The assay is described more in detail in Assays & Annotation.
Protein expression (score)
Each bar represents the highest expression score found in a particular group of tissues. For proteins where the
antibody staining pattern has been analyzed by knowledge-based annotation, protein expression scores are based
on a best estimate of the "true" protein expression, described more in detail under Assays & annotation. For genes
that are pending this extended review, the protein expression scores correspond to the staining profile of the
used antibody. For genes where more than one antibody has been used, a common 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 13 tissue groups, each consisting
of tissues with common functional features. Mouse-over function shows protein score for analyzed cell types found 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 could not be performed, 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.
RNA-seq data from 32 tissues are reported as mean FPKM (Fragments Per Kilobase gene model and Million reads),
corresponding to mean values of the different individual samples from each tissue type. Color-coding is based on 13 tissue
groups, each consisting of tissues with common functional features. 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 in 32 different tissues and include: tissue enriched, group enriched, tissue enhanced,
expressed in all, not detected and mixed.
GTEx dataset
RNA-seq data from 28 tissues are reported as median RPKM (reads per kilobase per million mapped reads), generated by the
Genotype-Tissue Expression (GTEx) consortium. 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 in 28 different tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, not detected and mixed.
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) (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.
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.
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)
SCAMPI predicted membrane proteins Predicted intracellular proteins Cancer-related genes 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 Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Predicted intracellular proteins Cancer-related genes 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 Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Predicted intracellular proteins Cancer-related genes 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 Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Predicted intracellular proteins Cancer-related genes 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 Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Predicted intracellular proteins Cancer-related genes 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 Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Predicted intracellular proteins Cancer-related genes 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 Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Predicted intracellular proteins Cancer-related genes 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 Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
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)
