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The cancer tissue page shows antibody staining in 20 different cancers. The assay and annotation is described here.
This page starts with information about the protein evidence and, when applicable, also protein class. Below the summary, a selection of four standard cancer tissue samples is displayed as representative of the overall staining pattern. From left: colorectal cancer, breast cancer, prostate cancer and lung cancer. An additional 5th image can be added as a complement.
The cancer tissue summary page shows antibody staining in 20 different cancers. The assay and annotation is described here.
For each cancer, the fraction of samples with antibody staining/protein expression level high, medium, low, or not detected are provided by the blue-scale color-coding (as described by the color-coding scale in the box to the right). The length of the bar represents the number of patient samples analyzed (max=12 patients). 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. The tooltip function displays additional data for the features in the staining summary view.
Next to the cancer staining data, the protein expression data of normal tissues or specific cell types corresponding to each cancer are shown and protein expression levels are indicated by the blue-scale color coding.
At the bottom of the page, a summary of the overall protein expression pattern across the analyzed cancer tissues as well as information about literature conformity are presented.
Several cases of squamous and basal cell carcinomas, gliomas, melanomas, thyroid and urothelial cancers along with a few cases of endometrial and liver cancers showed moderate to strong cytoplasmic positivity. Remaining cancer tissues were negative.
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
SMAD5 (HGNC Symbol)
Synonyms
Dwfc, JV5-1, MADH5
Description
SMAD family member 5 (HGNC Symbol)
Entrez gene summary
The protein encoded by this gene is involved in the transforming growth factor beta signaling pathway that results in an inhibition of the proliferation of hematopoietic progenitor cells. The encoded protein is activated by bone morphogenetic proteins type 1 receptor kinase, and may be involved in cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 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) (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.
SMAD5-001
SMAD5-002
SMAD5-003
SMAD5-004
SMAD5-005
SMAD5-008
SMAD5-010
SMAD5-201
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.
Q99717 [Direct mapping] Mothers against decapentaplegic homolog 5 Q68DB7 [Target identity:100%; Query identity:100%] Mothers against decapentaplegic homolog
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Predicted intracellular proteins Transcription factors beta-Hairpin exposed by an alpha/beta-scaffold Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
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GO:0000979 [RNA polymerase II core promoter sequence-specific DNA binding] GO:0001503 [ossification] GO:0001657 [ureteric bud development] GO:0001880 [Mullerian duct regression] GO:0002051 [osteoblast fate commitment] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0005057 [receptor signaling protein activity] GO:0005515 [protein binding] GO:0005622 [intracellular] GO:0005634 [nucleus] 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:0006468 [protein phosphorylation] GO:0007165 [signal transduction] GO:0007179 [transforming growth factor beta receptor signaling pathway] GO:0007281 [germ cell development] GO:0009880 [embryonic pattern specification] GO:0016021 [integral component of membrane] GO:0030218 [erythrocyte differentiation] GO:0030509 [BMP signaling pathway] GO:0030618 [transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity] GO:0031625 [ubiquitin protein ligase binding] GO:0035556 [intracellular signal transduction] GO:0043234 [protein complex] GO:0045669 [positive regulation of osteoblast differentiation] 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:0051216 [cartilage development] GO:0060048 [cardiac muscle contraction] GO:0060348 [bone development] GO:0060395 [SMAD protein signal transduction] 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]
Q99717 [Direct mapping] Mothers against decapentaplegic homolog 5 Q68DB7 [Target identity:100%; Query identity:100%] Mothers against decapentaplegic homolog
Show all
Predicted intracellular proteins Transcription factors beta-Hairpin exposed by an alpha/beta-scaffold Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0005057 [receptor signaling protein activity] GO:0005515 [protein binding] GO:0005622 [intracellular] GO:0005634 [nucleus] 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:0007165 [signal transduction] GO:0007179 [transforming growth factor beta receptor signaling pathway] GO:0009880 [embryonic pattern specification] GO:0016021 [integral component of membrane] GO:0030509 [BMP signaling pathway] GO:0030618 [transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity] GO:0031625 [ubiquitin protein ligase binding] GO:0035556 [intracellular signal transduction] GO:0043234 [protein complex] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0046872 [metal ion binding] GO:0060395 [SMAD protein signal transduction] GO:0071141 [SMAD protein complex] 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]
