v6.0 2019 May
An integrated database of Homo sapiens genomic data
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For a given Gene (or List of Genes) show any associated Pathway(s) (Data Source: KEGG or REACTOME). Keywords: pathways, metabolism, cascade
Search for Genes in a specified organism that are associated with a particular Gene Ontology (GO) annotation.
Search for GO annotations for a particular gene (or List of Genes).
For a given Gene (or List of Genes) returns a list of SNPs associated with the Gene in GWAS experiments. Results can be constrained by P-value [Format Examples: 0.05 or 2.0E-6; default = 0.01] or Phenotype [Example: *diabetes* or *obesity* or try typing your keyword to bring up the autocomplete options] [Keywords: genome wide association, study, studies, disease]
Show expression for a gene or list of genes associated with a specific tissue(s). Optionally constrain the P-value. Data source: The Gene Expression Atlas (http://www.ebi.ac.uk/gxa/). Keywords: expression, expressed, Genes, Disease state, P value, T statistic.
For a given Gene A (or List A of Genes) show any interactions that occur with gene B (or List B of Genes)
For a given Gene (or List of Genes) in named organism (default: Human) returns the orthologues in a different organisms. [keywords: homologue, homolog, paralogue, paralogue, ortholog]
For a specified gene, show physical and genetic interaction partners. Optionally constrain to show just physical or genetic interactions or interactions determined by a specific method.
Show the chromosome and the chromosome location of a particular gene.
For a specified gene or genes, show genes that interact with this gene that are also expressed in the specified tissue. (Interactors could be physical or genetic; Expression is based on tissue expression from the Protein Atlas Project and should be further interrogated for reliability level).
For a given Gene (or List of Genes) returns a list of associated diseases (source: OMIM)
Show expression for a gene or list of genes. Optionally constrain the P-value and the T-statistic. The results can also be optionally filtered on organism part, cell type or disease state. Data source: The Gene Expression Atlas (http://www.ebi.ac.uk/gxa/). Keywords: Expression, Genes, Organism part, Disease state, Cell type, P value, T statistic.
For a given Pathways show any Genes associated with the Pathway(s) in a given organism (Data Source: KEGG or REACTOME). [NOTE: Organism is an optional filter which is ON by default but can be turned OFF to show genes from all organisms.] Keywords: Pathway, KEGG, Reactome
For a given SNP (or List of SNPs) returns GWAS results featuring that SNP (where applicable, associated Gene is also returned). Results can be filtered by P-value [Format Examples: 0.01 or 2.0E-6; default = 0.01], Author [Format: type the start of a Author to bring up autocomplete options. NOTE: This Filtr is OFF by default. Click to turn ON] OR Phenotype [Example: *diabetes* or *obesity* or type the start of a keyword to bring up autocomplete options] [Keywords: genome wide association, study, studies, disease]
For a given Gene (or List of Genes) returns the corresponding Protein(s) products.
For a gene or list of genes show the diesases (from OMIM) and the related Human Phenotype Ontology annotations. Note that the publication is evidence for the HPO annotation.
For a given human disease returns a list of associated or implicated human genes (source: OMIM)
Show expression for a gene or list of genes associated with specific disease state(s). Optionally constrain the P-value. Data source: The Gene Expression Atlas (http://www.ebi.ac.uk/gxa/). Keywords: expression, expressed, Genes, Disease state, P value, T statistic.
For a specified organism and chromosomal location show all genes, transcripts and exons
Show the genes located between two points on a chromosome. [Keywords: span, region, co-ordinates]
Retrieve details of protein complexes that the specified protein is known to be part of.
For a given human gene returns tissues in which the corresponding protein has been identified. Data Source: Protein Atlas
For a Gene (or List of Genes) with GO Annotation, returns a subset of genes with that particular GO anotation. Used to filter lasrge Gene sets by GO term.
For a gene or gene list return those that interact with genes in a specified pathway.
For a given Gene (or List of Genes) in named organism (default: Human) returns the orthologues in a different organisms (default : Mouse), alleles (MGI) and associated (major) Phenotypic terms (MGI). [keywords: homologue, homolog, paralogue, paralogue, ortholog, allele, strain, phenotype]
For a specified gene or gene list, show the tissue expression according to the Illumina body map data. (https://www.ebi.ac.uk/gxa/experiments/E-MTAB-513/Results)
Search GWAS experiments and return SNPs and associated genes. Searchable fields include: First Author, Pub Med ID, phenotype and Phenotype [Example: *diabetes* or *obesity* or try typing your keyword to bring up autocomplete options]. Filter by p-value cut-off [Format Examples: 0.01 or 2.0E-6; default = 0.01]. [Keywords: genome wide association, study, studies, disease] NOTE: THIS TEMPLATE ONLY RETURNS SNPs THAT ALSO HAVE AN ASSOCIATED GENE. USE TEMPLATE "GWAS term --> SNP + Associated gene if available" FOR ALL SNPS.
For a specified protein, show physical and genetic interaction partners. Optionally constrain to show just physical or genetic interactions or interactions determined by a specific method.
For a given Gene A (or List A of Genes) show any associated Pathway(s) in common with Gene B (or List B of Genes). Datasource: KEGG or REACTOME. Keywords: pathways, cascade, metabolism, reaction
For a gene, show alleles and any associated diseases. (Data from ClinVar: https://www.ncbi.nlm.nih.gov/clinvar/)
Retrieve details of protein complexes that the specified gene is known to be part of.
Admin template to display GWAS results in Gene report pages. Do not use. Instead use: Gene --> GWAS hit
For a particular gene, search for overlapping genes.
For a specified gene or list of genes, show the tissue expression levels according to the GTex RNA-seq data (https://www.gtexportal.org/home/)
Returns a list of publications that reference a specified gene. References are loaded from NCBI for Human, Mouse and Rat.
for a specified protein or list proteins give the protein sequence and length.
For a given mouse Gene (or List of Genes) returns the alleles (MGI) and associated (major) Phenotypic terms (MGI). [keywords: allele, strain, phenotype]
Show proteins which have a specified protein domain or family.
For a given organism (default = H. sapiens) displays all proteins.
For a given macromolecular complex, retrieve Gene Ontology annotations and references for the complex as a whole; also retrieve the subunits of the complex, their stoichiometry, and their biological roles in the complex.
For a given human disease returns a list of associated or implicated human genes and orthologues in other species (mouse and rat. Default:mouse) (disease source: OMIM)
For a given phenotype (as defined in the mammalian phenotype ontology) returns a list of mouse alleles (MGI) which display these phenotypes. Keywords: phenotype, strain, allele, mouse, knockout, deletion, mutation
Show the gene that codes for the following protein, with its chromosomal location and length.
Show protein domains and families for the specified protein.
For a gene or list of genes show the Human Phenotype Ontology annotations.
For a given human tissue returns a list of Genes which are localised in the tissue. Optional filters are expression level and experimental confidence.
For a given Protein (or List of Proteins), returns the associated Gene Ontology (GO) terms. Optionally, you can specify Ontology category (eg. cellular_component, molecular_function, biological_process: OFF returns All).
Show protein domain information for the proteins of a specified gene.
For a gene or list of genes show significant single-tissue cis-E-QTL SNPs (GTex data)
For a specified tissue, show the gene expression levels according to the GTex RNA-seq data (https://www.gtexportal.org/home/)
For a pathway and dataset, show all proteins.
For a specified tissue or tissue list, show gene expression according to the Illumina body map data. (https://www.ebi.ac.uk/gxa/experiments/E-MTAB-513/Results)
For a given macromolecular complex, show the participating molecules.
For a given Protein (or List of Proteins), returns the associated genes and homologues.
For a given Phenotype (or List of Phenotypes) links mouse genes (with alleles displaying this phenotype) to orthologous genes (Use optional filter to return only human orthologues). [keywords: homologue, homolog, paralogue, paralogue, ortholog, allele, strain, phenotype]
For given MeSH term show all publications.
For a specified disease, show the Human Phenotype Ontology terms.
Search GWAS experiments and return SNPs and associated genes. Searchable fields include: First Author, Pub Med ID, phenotype and Phenotype [Example: *diabetes* or *obesity* or try typing your keyword to bring up autocomplete options]. Filter by p-value cut-off [Format Examples: 0.01 or 2.0E-6; default = 0.01]. [Keywords: genome wide association, study, studies, disease]
Show alleles associated with a specific disease(s). Data from ClinVar (https://www.ncbi.nlm.nih.gov/clinvar).
For a gene or list of genes, show whether it (or they) are annotated to any Human Phenotype Ontology terms where the parent term is the term given. (i.e will return any genes from the list which are annotated to the parent term or any of it's child terms. If only one gene is given, will return results if the gene is annotated to the parent term or any of it's child terms).
