v1.4
An integrated data warehouse for the Bovine Genome Database
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Given a gene id or gene symbol, retrieve the chromosomal coordinates.
Given a bovine gene id or symbol, retrieve transcripts and expression levels, optionally filtered by tissue and/or expression level.
Given a gene id or symbol, retrieve GO terms. Be sure to view the Qualifier column for genes annotated as "NOT".
Given a SNP rsID, retrieve ids (AnimalQTLdb) of overlapping QTL and traits.
Given a chromosome id and coordinates, retrieve genes.
Given a tissue, retrieve bovine transcript ids and expression values.
Given a bovine gene id, retrieve transcripts, expression levels and RNAseq metadata.
Given a bovine SNP rsID, retrieve chromosome location.
Given a gene id or symbol, retrieve pathways. The pathway data sources retrieved may be affected by the input id (RefSeq, Ensembl or gene symbol).
Given a gene id, retrieve variants and their consequences.
Given a bovine SNP rsID, retrieve gene. No rows will be returned if the SNP is not within a gene.
Given a gene id or symbol, retrieve publications.
Given a gene id or symbol in the selected organism, retrieve homologues. Optionally select homologue type.
Given gene id or symbol, retrieve interacting genes.
Given a GO term (e.g. DNA binding) or GO identifier (e.g. GO:0003677), retrieve genes. Wildcards (*) are allowed (e.g. *muscle*).
Given a chromosome id, retrieve genes and their locations.
Given a bovine trait, retrieve QTL id (AnimalQTLdb) and chromosomal location.
Given a gene id or symbol, retrieve transcript ids, locations and exon locations.
Given a gene id, retrieve proteins (UniProt) and protein domains.
Given an organism and gene set, retrieve all genes and their locations.
Given a gene id or symbol, retrieve Reactome pathways.
Given a gene id or symbol in the selected organism, retrieve GO terms and homologues. Optionally select homologue type.
Given a bovine SNP alias ID, such as ssID or an array id, retrieve dbSNP rsID.
Given a bovine transcript id, retrieve expression values and metadata.
Given an organism, retrieve all transcripts with genes and database cross references. Multiple gene sets may be retrieved, and can be filtered in the output.
Given a gene id or symbol in the specified non-bovine organism, retrieve homologous bovine genes, transcripts and expression values. Optionally select homologue type.
Given a gene id in organism 1, retrieve homologues in organism 2 and pathways for the homologues. Optionally select homologue type.
Given a bovine QTL id (AnimalQTLdb), retrieve SNPs within QTL region.
Given a bovine dbSNP rsID, retrieve SNP Alias IDS.
Given a gene id, retrieve database cross reference id (e.g. RefSeq to Ensembl or vice versa).
Given a gene source (e.g. RefSeq or Ensembl), retrieve all gene ids. Use this to create a single-gene-set background list for enrichment.
Given a gene id or symbol from the selected non-bovine organism, retrieve bovine homologues and pathways. Optionally select homologue type.
Given a bovine gene id, retrieve transcripts, expression levels, metadata and Brenda Tissue Ontology.
Given a non-human Gene id, retrieve human homologues and pathway information for those homologues. Optionally select homologue type.
Given a gene id or symbol, retrieve homologues.
Given a gene id or gene symbol, retrieve proteins (UniProt).
Given a bovine QTL id (AnimalQTLdb), retrieve transcripts within QTL region. A list of transcripts can be saved and used in an expression template query. No rows will be returned if there are no transcripts.
Given a gene id or symbol, retrieve transcript ids and coding sequences.
Given a QTL id from AnimalQTLdb, retrieve trait and Vertebrate Trait Ontology.
Given a protein id (UniProt), retrieve genes and GO.
Given a gene id, retrieve gene symbol and description.
Given a transcript id, retrieve protein id (from gene set, not UniProt).
Given a protein id (UniProt), retrieve publications.
Given a bovine trait, retrieve QTL id from AnimalQTLdb.
Given a bovine transcript ID, retrieve expression values and metadata, optionally filtered by tissue and expression values.
Retrieve all gene ids and database cross reference ids for the specified organism and gene source.
Given a transcript ID, retrieve gene id and GO terms.
Given an organism, retrieve proteins with publications.
Given protein domain name (InterPro), retrieve information about protein domains. Wildcards (*) are allowed.
Given a bovine QTL id (AnimalQTLdb), retrieve genes within QTL region. You can create a gene list to use in a gene template query. No rows will be returned if there are no genes.
Given an organism, retrieve all protein ids (UniProt).
Given an InterPro id, retrieve proteins and genes.
Given a gene id, retrieve transcript id(s).
For a given organism, retrieve all mRNAs and proteins along with their lengths. All gene sources are provided.
Given a gene id or symbol in the selected organism, retrieve human orthologues.
Given a transcript id, retrieve gene id.
Given an organism, retrieve all miRNAs and their locations.
Given a transcript id, retrieve gene id and pathways.
Given a gene id or symbol, retrieve transcript and protein ids (from the gene set, not UniProt).
Given a bovine SNP rsID, retrieve SNP alias IDs and sources.
Given an InterPro protein domain name, retrieve proteins and genes for an organism. Wildcards (*) are allowed.
Given a gene source and organism, retrieve all gene ids, gene symbols and transcript ids.
Given a chromosome id and coordinates, retrieve miRNAs.
Given a gene symbol, retrieve gene id from the specified gene set.
Given a protein id (UniProt), retrieve corresponding gene and location of gene.
Given a transcript id, retrieve protein id.
Given a gene id, retrieve publications.
Given a gene id, retrieve transcripts.
Given a gene id, retrieve transcripts and proteins.
