Search: protein_class:COSMIC Amplifications

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The search result lists the genes found by the search function. The list can be limited to only include genes with antibodies. The list can also be limited to only include genes with supported validation or reliablity, defined as premium genes.

The show/hide columns function can be used to add columns to the search result list, with information about:

the gene (synonyms, Ensembl gene identifier (ENSG), gene description, chromosomal location and protein class),
evidence (Evidence summary, HPA, UniProt and MS evidence),
annotations (the reliablity of the annotated protein expression using immunohistochemically (IH) stained on human tissues, the reliablity of the annotated protein expression in immunofluorescently (IF) stained human cell lines, tissue specificity (the distribution of antibody staining or protein expression in human cell types), cell line specificity (the distribution of RNA abundance in cell lines) and subcellular location (based on immunofluorescent staining of cell lines)),
protein expression in organs, such as digestive tract or placenta. The different colored areas of the bar represent the fraction of the analysed cell types in that organ with a certain relative level of protein expression/antibody staining (intensity of the color). A red color scale represents antibody staining while a blue color scale represents annotated protein expression.

To use more complex search queries using "Fields", see examples.

The Human Protein Atlas data for each gene is accessed by clicking on the gene of interest. The four different atlases (tissue, subcell, cell & cancer) can be accessed through the corresponding thumbnail images.

Data for all genes included in the search result can be downloaded in three different formats, links are found in the upper right corner of the search result page:

A tab-separated file with the search results can be retrieved by clicking the "TAB"-link.
An RDF-file containing structured nanopublication data for the tissue annotations can be retrieved by clicking the "RDF"-link.
An XML-file with more extensive data (including protein expression data (in normal and tumor tissues and in cell lines), antigen sequences, Western blot data for antibodies, protein array data for antibodies, RNA-seq data, external references such as UniProt identifiers, and more (see XSD)) for up to 10000 genes in a search result can be retrieved by clicking the "XML"-link.

- Gene - Geneⁱ Gene name according to HGNC. Gene synonymⁱ Synonyms according to Ensembl and Entrez. Ensembl gene idⁱ Gene identification number according to Ensembl. Gene descriptionⁱ Gene description according to HGNC. Chromosome Chromosome position Protein classⁱ Protein class the gene product belongs to according to selected gene lists. List of protein classes. - Evidence - Evidence (summary)ⁱ 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. HPA evidence UniProt evidence MS evidence - Atlas - Tissue Cell Pathology	- Annotation - Antibodyⁱ Antibodies used for immunohistochemistry (results presented in Tissue and Pathology Atlas) and immunocytochemistry/IF (results presented in Cell Atlas) assays. The assays are described in detail in Assays & annotation. Read more Reliability (IH)ⁱ Reliability score, 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. Read more Reliability (Mouse Brain)ⁱ Reliability score, divided into Supported or Uncertain, is set for all genes and indicates the level of reliability of the analyzed protein expression pattern based on available protein/RNA/gene characterization data. Read more Reliability (IF)ⁱ Reliability score, divided into Enhanced, Supported, Approved, or Uncertain, is evaluated in cell lines 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. Read more IH abundance (Normal Tissue)ⁱ A summary of protein expression levels in the analyzed normal tissues. Annotation of protein expression is described in detail in Assays & annotation. RNA abundance (Normal Tissue)ⁱ A summary of mRNA abundance in the analyzed normal tissues. The RNA-seq assay is described in detail in Assays & Annotation. Subcellular locationⁱ Subcellular localization according to immunocytochemistry/IF analysis. - RNA - Cancer prognostic p-valueⁱ P-value of Kaplan-Meier analysis for all cancers where high expression of the gene is associated with favorable prognosis (green) or unfavorable prognosis (red) with regard to patient survival. RNA cancer categoryⁱ RNA cancer category is based on analysis of RNA-seq data from The Cancer Genome Atlas (TCGA). RNA tissue categoryⁱ RNA category is based on mRNA expression levels in the analyzed tissue samples (RNA assay description). RNA tissue specificity scoreⁱ RNA TS indicates tissue specificity (TS) score for tissues with elevated RNA expression, calculated as fold change to the next highest tissue. Read more RNA tissue specific TPMⁱ RNA TS TPM indicates RNA level reported as mean TPM (transcripts per million), in tissues with elevated RNA expression. RNA tissue TPM max in non-specificⁱ Highest RNA level, reported as mean TPM (transcripts per million), among tissues that do not have elevated RNA expression. RNA cell line categoryⁱ RNA category is based on mRNA expression levels in the analyzed tissue samples (RNA assay description). RNA cell line specificity scoreⁱ RNA CS indicates cell specificity (CS) score for cell lines with elevated RNA expression, calculated as fold change to the next highest cell line. Read more RNA cell line specific TPMⁱ RNA CS TPM indicates RNA level (TPM) in cell lines with elevated RNA expression. Read more	- Organ - Brain Bone marrow & immune system Liver & gallbladder Gastrointestinal tract Respiratory system Muscle tissues Breast and female reproductive system Pancreas Male reproductive system Kidney & urinary bladder Adipose & soft tissue Endocrine tissues Skin

Gene name according to HGNC.

Gene description according to HGNC.

Protein class the gene product belongs to according to selected gene lists. List of protein classes.

Subcellular localization according to immunocytochemistry/IF analysis.

P-value of Kaplan-Meier analysis for all cancers where high expression of the gene is associated with favorable prognosis (green) or unfavorable prognosis (red) with regard to patient survival.

RNA category is based on mRNA expression levels in the analyzed tissue samples (RNA assay description).