FAANGMine: Template queries page

Given a gene id or gene symbol, retrieve the chromosomal coordinates.

Given a gene id or symbol, retrieve GO terms. Be sure to view the Qualifier column for genes annotated as "NOT".

Given a chromosome id and coordinates, retrieve genes.

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).

Gene --> Homologues

Given a gene id or symbol in the selected organism, retrieve homologues. Optionally select homologue type and organism.

SNP rsID --> Chromosome Location

Given a SNP rsID, retrieve chromosome location.

Gene --> Interacting genes

Given gene id or symbol, retrieve interacting genes.

SNP rsID --> Gene

Given a SNP rsID and organism, retrieve gene. No rows will be returned if the SNP is not within a gene.

Gene ID --> Variant Consequences

Given an Ensembl gene id, retrieve variants and their consequences.

Gene --> Publications

Given a gene id or symbol, retrieve publications.

Gene Source and Organism --> Gene IDs

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.

SNP Alias ID --> dbSNP rsID

Given a SNP alias ID, such as ssID or an array id, retrieve dbSNP rsID.

Chromosome --> genes

Given a chromosome id, retrieve genes and their locations.

GO Term --> Genes

Given a GO term (e.g. DNA binding) or GO identifier (e.g. GO:0003677), retrieve genes. Wildcards (*) are allowed (e.g. *muscle*).

Gene --> Transcripts + Exons

Given a gene id or symbol, retrieve transcript ids, locations and exon locations.

Trait --> QTL id --> Chromosomal Location

Given a bovine, pig, sheep or chicken trait, retrieve QTL id (AnimalQTLdb) and chromosomal location.

Gene --> Protein (UniProt) and Protein Domains

Given a gene id, retrieve proteins (UniProt) and protein domains.

Gene --> Homologues --> Pathways

Given a gene id or symbol from one organism, retrieve homologues and pathways. Optionally select homologue type and organism. Check the Data Source page to find out which organisms have homologues and pathways.

Gene --> Reactome Pathway

Given a gene id or symbol, retrieve Reactome pathways.

Gene Source and Organism --> Genes and Chromosomal location

Given an organism and gene set, retrieve all genes and their locations.

SNP (rsID) --> SNP Alias IDs

Given dbSNP rsID, retrieve SNP Alias IDS and sources.

Organism --> All proteins

Given an organism, retrieve all protein ids (UniProt).

Organism --> Transcripts + Genes + Database Cross Reference IDs

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.

Gene ID --> Database Cross Reference ID (e.g RefSeq to Ensembl)

Given a gene id, retrieve database cross reference id (e.g. RefSeq to Ensembl or vice versa).

Trait --> QTL

Given a bovine, pig, sheep or chicken trait, retrieve AnimalQTLdb QTL.

Gene --> Proteins (UniProt)

Given a gene id or gene symbol, retrieve proteins (UniProt).

Protein --> GO Terms

Given a protein id (UniProt), retrieve genes and GO.

QTL --> Genes

Given a bovine, pig, sheep or chicken 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.

QTL --> Trait and VTO

Given a bovine, pig, sheep or chicken QTL id from AnimalQTLdb, retrieve trait and Vertebrate Trait Ontology.

QTL --> Transcripts

Given a bovine, pig, sheep or chicken QTL id (AnimalQTLdb), retrieve transcripts within QTL region. No rows will be returned if there are no transcripts.

Gene --> Human Homologues --> Human Pathways

Given a non-human Gene id, retrieve human homologues and pathway information for those homologues. Optionally select homologue type.

Genome Assembly --> Chromosome IDs and Lengths

Given a genome assembly version, retrieve primary chromosome ids used in FAANGMine, alternative ids and chromosome lengths.

Gene --> Homologues for report page

Given a gene id or symbol, retrieve homologues.

Gene Source and Organism --> Genes and Database Cross Reference IDs

Retrieve all gene ids and database cross reference ids for the specified organism and gene source.

Protein --> Publications

Given a protein id (UniProt), retrieve publications.

Trait --> VTO Term

Given a trait and organism, retrieve VTO term. Remove trait name constraint to retrieve all traits and VTO terms.

Gene --> Cross References

Gene --> Human Orthologues

Given a gene id or symbol in the selected organism, retrieve human orthologues.

Gene id --> Symbol + Description

Given a gene id, retrieve gene symbol and description.

Transcript ID --> Gene ID

Given a transcript id, retrieve gene id.

Transcript ID -> Protein

Given a transcript id, retrieve protein id (from gene set, not UniProt).

Gene --> Transcript id + coding sequence

Given a gene id or symbol, retrieve transcript ids and coding sequences.

Gene ID --> Transcript ID(s)

Given a gene id, retrieve transcript id(s).

InterPro Name --> Protein domains and families

Given protein domain name (InterPro), retrieve information about protein domains. Wildcards (*) are allowed.

Organism --> Proteins (UniProt) and Publications.

Given an organism, retrieve UniProt proteins with publications.

QTL ID --> SNP ID

Given a bovine, pig, sheep or chicken QTL ID from AnimalQTLdb, retrieve SNPs within the QTL region.

Gene ID --> Symbol

Gene --> Transcript + Proteins

Given a gene id or symbol, retrieve transcript and protein ids (from the gene set, not UniProt).

Transcript ID --> Gene ID --> GO terms

Given a transcript ID, retrieve gene id and GO terms.

Organism --> Genes + mRNA + Protein

For a given organism, retrieve all mRNAs and proteins along with their lengths. All gene sources are provided.

Transcript ID --> Non synonymous variants

Given an Ensembl transcript ID, retrieve non-synonymous coding variants.

Transcript id --> Gene id --> Pathways

Given a transcript id, retrieve gene id and pathways.

Organism --> All miRNAs

Given an organism, retrieve all miRNAs and their locations.

Organism --> All QTL

Given an organism, retrieve all QTL ids, along with traits and chromosome locations.

Transcripts

Given a gene id, retrieve transcripts.

InterPro ID --> Proteins --> Genes

Given an InterPro id, retrieve proteins and genes.

Transcripts --> Protein

Given a gene id, retrieve transcripts and proteins.

Protein --> Gene

Given a protein id (UniProt), retrieve corresponding gene and location of gene.

Chromosome location --> miRNAs

Given a chromosome id and coordinates, retrieve miRNAs.

Gene Source and Organism --> Genes and Transcript ids

Given a gene source and organism, retrieve all gene ids, gene symbols and transcript ids.

Gene symbol --> Gene id

Given a gene symbol, retrieve gene id from the specified gene set.

Publications

Given a gene id, retrieve publications.

InterPro Name --> Proteins --> Genes

Given an InterPro protein domain name, retrieve proteins and genes for an organism. Wildcards (*) are allowed.

Proteins

Given a transcript id, retrieve protein id.

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