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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):
Expressed in all
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 expression at variable levels in several different cell types.
IMMUNOHISTOCHEMISTRY DATA RELIABILITY
Data reliability descriptioni
Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.
Pending external verification.
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.
Melanoma, several cases of colorectal and urothelial cancer as well as a few cases of endomatrial and lung cancers showed moderate to strong cytoplasmic immunoreactivity. Remaining cancer tissues were weakly stained or 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
SOS1 (HGNC Symbol)
Synonyms
GF1, GINGF, HGF
Description
SOS Ras/Rac guanine nucleotide exchange factor 1 (HGNC Symbol)
Entrez gene summary
This gene encodes a protein that is a guanine nucleotide exchange factor for RAS proteins, membrane proteins that bind guanine nucleotides and participate in signal transduction pathways. GTP binding activates and GTP hydrolysis inactivates RAS proteins. The product of this gene may regulate RAS proteins by facilitating the exchange of GTP for GDP. Mutations in this gene are associated with gingival fibromatosis 1 and Noonan syndrome type 4. [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.
SOS1-001
SOS1-003
SOS1-004
SOS1-201
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.
Q07889 [Direct mapping] Son of sevenless homolog 1
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SPOCTOPUS predicted membrane proteins Predicted intracellular proteins Plasma proteins RAS pathway related proteins Cancer-related genes Mutated cancer genes Mutational cancer driver genes Disease related genes Protein evidence (Ezkurdia et al 2014)
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GO:0000165 [MAPK cascade] GO:0001782 [B cell homeostasis] GO:0001942 [hair follicle development] GO:0002260 [lymphocyte homeostasis] GO:0003007 [heart morphogenesis] GO:0003209 [cardiac atrium morphogenesis] GO:0003344 [pericardium morphogenesis] GO:0003677 [DNA binding] GO:0005085 [guanyl-nucleotide exchange factor activity] GO:0005088 [Ras guanyl-nucleotide exchange factor activity] GO:0005089 [Rho guanyl-nucleotide exchange factor activity] GO:0005096 [GTPase activator activity] GO:0005515 [protein binding] GO:0005829 [cytosol] GO:0005886 [plasma membrane] GO:0007165 [signal transduction] GO:0007173 [epidermal growth factor receptor signaling pathway] GO:0007264 [small GTPase mediated signal transduction] GO:0007265 [Ras protein signal transduction] GO:0007296 [vitellogenesis] GO:0007411 [axon guidance] GO:0008286 [insulin receptor signaling pathway] GO:0014069 [postsynaptic density] GO:0017124 [SH3 domain binding] GO:0033081 [regulation of T cell differentiation in thymus] GO:0035023 [regulation of Rho protein signal transduction] GO:0035264 [multicellular organism growth] GO:0038095 [Fc-epsilon receptor signaling pathway] GO:0038128 [ERBB2 signaling pathway] GO:0042129 [regulation of T cell proliferation] GO:0043025 [neuronal cell body] GO:0043065 [positive regulation of apoptotic process] GO:0043547 [positive regulation of GTPase activity] GO:0045742 [positive regulation of epidermal growth factor receptor signaling pathway] GO:0046982 [protein heterodimerization activity] GO:0048011 [neurotrophin TRK receptor signaling pathway] GO:0048514 [blood vessel morphogenesis] GO:0050900 [leukocyte migration] GO:0051056 [regulation of small GTPase mediated signal transduction] GO:0051057 [positive regulation of small GTPase mediated signal transduction] GO:0060021 [palate development] GO:0061029 [eyelid development in camera-type eye] GO:0061384 [heart trabecula morphogenesis] GO:1904693 [midbrain morphogenesis] GO:2000973 [regulation of pro-B cell differentiation]
G5E9C8 [Direct mapping] Son of sevenless homolog 1; Son of sevenless homolog 1 (Drosophila), isoform CRA_d
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SPOCTOPUS predicted membrane proteins Predicted intracellular proteins RAS pathway related proteins Cancer-related genes Mutated cancer genes Mutational cancer driver genes Protein evidence (Ezkurdia et al 2014)
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GO:0003677 [DNA binding] GO:0005085 [guanyl-nucleotide exchange factor activity] GO:0005089 [Rho guanyl-nucleotide exchange factor activity] GO:0005622 [intracellular] GO:0007264 [small GTPase mediated signal transduction] GO:0035023 [regulation of Rho protein signal transduction] GO:0043547 [positive regulation of GTPase activity] GO:0046982 [protein heterodimerization activity]
C9K0N6 [Direct mapping] Son of sevenless homolog 1
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Predicted intracellular proteins RAS pathway related proteins Cancer-related genes Mutated cancer genes Mutational cancer driver genes Protein evidence (Ezkurdia et al 2014)
Q07889 [Direct mapping] Son of sevenless homolog 1
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SPOCTOPUS predicted membrane proteins Predicted intracellular proteins Plasma proteins RAS pathway related proteins Cancer-related genes Mutated cancer genes Mutational cancer driver genes Disease related genes Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
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GO:0000165 [MAPK cascade] GO:0003677 [DNA binding] GO:0005085 [guanyl-nucleotide exchange factor activity] GO:0005088 [Ras guanyl-nucleotide exchange factor activity] GO:0005089 [Rho guanyl-nucleotide exchange factor activity] GO:0005096 [GTPase activator activity] GO:0005515 [protein binding] GO:0005829 [cytosol] GO:0005886 [plasma membrane] GO:0007165 [signal transduction] GO:0007173 [epidermal growth factor receptor signaling pathway] GO:0007264 [small GTPase mediated signal transduction] GO:0007265 [Ras protein signal transduction] GO:0007411 [axon guidance] GO:0008286 [insulin receptor signaling pathway] GO:0035023 [regulation of Rho protein signal transduction] GO:0038095 [Fc-epsilon receptor signaling pathway] GO:0038128 [ERBB2 signaling pathway] GO:0043065 [positive regulation of apoptotic process] GO:0043547 [positive regulation of GTPase activity] GO:0046982 [protein heterodimerization activity] GO:0050900 [leukocyte migration] GO:0051056 [regulation of small GTPase mediated signal transduction]
The Human Protein Atlas project is funded
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