Given a gene id or symbol, retrieve GO terms. Be sure to view the Qualifier column for genes annotated as "NOT", which you might want to filter out of your results.

Given a gene id, retrieve gene expression values. Optionally constrain by expression level, Brenda Tissue Ontology name, SRA Experiment id, BioSample id, or to FAANG data only. Constraining by organism may speed up the search. However, adding too many constraints simultaneously may result in no output.

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 Brenda Tissue Ontology name, organism and gene source, retrieve genes and expression values.

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

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

Given a gene id, retrieve gene expression values.

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

Given a gene id or symbol, retrieve publications.

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

Given an SRA experiment id and gene source, retrieve genes and expression values.

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

Given a Gene ID, retrieve overlapping and nearby histone modification marks. The "Symbol" column in the output shows details, including modification, tissue, narrow or broad peak (N or B) and genome location (chromosome:start-end). Currently FAANGMine has histone modification marks identified by ChiP-seq only for horse.

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

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

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

Given a bioproject id associated with a chromatin state data source, retrieve specimen and analysis tags. The specimen tags allow you to perform queries on samples used in experiments that were input into chromatin state prediction.

Given gene id or symbol, retrieve interacting genes.

Given an organism, retrieve all FAANG experiments.

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.

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

Given a histone modification mark identifier, retrieve all overlapping features.

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

List all FAANG ChIP-seq experiments for a given organism.

Given a chromosome id and coordinates, retrieve genes.

Given an organism, retrieve all FAANG analyses.

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

Given a histone modification mark identifier, retrieve overlapping or nearby gene.

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

Given a BioSample ID, retrieve RNA-seq experiment, genes and expression levels.

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.

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

Given a transcript id, retrieve gene id.

Given an organism, retrieve UniProt proteins with publications.

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

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

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

Given an SNV rsID, retrieve chromosome location.

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

Given a gene id or symbol, retrieve Reactome pathways.

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

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

Given a transcript id, retrieve gene id and pathways.

Given in identifier for a virtual pooled BioSample, retrieve component BioSample IDs.

Given a gene id, retrieve transcripts.

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

Given a FAANG analysis accession, retrieve tissue, biosample ids, and other analysis metadata. For analyses that pool results from experiments, there will be a BioSample ID for a virtual pooled sample, as well as component BioSample IDs.

Given a gene id, retrieve publications.

Given rsID, retrieve SNV Alias IDs and sources.

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.

Given a gene id, retrieve transcripts and proteins.

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

Given a chromosome id and optional coordinates, retrieve miRNAs.

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

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

Given a transcript id, retrieve protein id.

Given a protein id (UniProt), retrieve publications.

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

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

Given an InterPro id, retrieve proteins and genes.

Given a Specimen Tag, retrieve RNA-seq experiment, genes and expression levels. A Specimen Tag is an identifier that we assign to BioSamples from the same individual/tissue that were used in different types of experiments (e.g. RNA-seq, ChIP-seq, ATAC-seq). Sometimes the Specimen Tag is equivalent to the BioSample id. However when specimens from the same individual/tissue were submitted as a different BioSample for each type of experiment, we assign an identifier that combines the tissue and individual id so that the combined results for this individual/tissue can be investigated.

Given an organism, retrieve all miRNAs and their locations.

Given a specimen tag, retrieve biosample(s), experiment(s) and other metadata. A Specimen Tag is an identifier that we assign to BioSamples from the same individual/tissue that were used in different types of experiments (e.g. RNA-seq, ChIP-seq, ATAC-seq). Sometimes the Specimen Tag is equivalent to the BioSample id. However when specimens from the same individual/tissue were submitted as a different BioSample for each type of experiment, we assign an identifier that combines the tissue and individual id so that the combined results for this individual/tissue can be investigated.

Given a chromosome id, retrieve genes and their locations.

Given a gene id or symbol, retrieve homologues.

Given a gene id, retrieve gene symbol and description.

List all FAANG RNA-seq experiments for a given organism.

Given an experiment accession, retrieve Biosample ID and specimen tag.

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

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

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

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

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

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

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

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

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