FAANGMine

The source of gene annotations in FAANGMine are NCBI (RefSeq) and Ensembl.

Query for genes:

• Gene    GO terms
• Gene    Publications
• Gene    Chromosomal location
• Gene    Transcript + Proteins
• Transcript ID -> Protein
• Chromosomal location    genes
• Gene symbol    Gene id
• Transcript ID    Gene ID

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Gene expression values (FPKM and TPM) were computed using RNAseq from gene atlas expression and FAANG (Functional Annotation of Animal Genomes) datasets. The Data Source page lists expression datasets available for each species.

Query for expression:

• Gene ID    Gene Expression
• Tissue    Genes and Expression Values
• Gene    Expression
• SRA Experiment    Genes and Expression Values
• BioSample ID    RNA-seq experiment, Genes and Expression Values
• Specimen Tag    RNA-seq experiment, Genes and Expression Values

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This template category is for data and metadata generated by the Functional Annotation of Animal Genomes (FAANG) Consortium. FAANG data includes RNA-seq based gene expression levels; ChIP-seq based histone modification marks and CTCF binding sites, ATAC-seq based open chromatin regions, DNaseI hypersensitive sites, topologically associated domains, A/B compartments and chromatin states. Sequence ontology terms used are "histone_binding_site" for histone modifications, "biological_region" for A/B compartments, "regulatory_region" for chromatin states, "CTCF_binding_site", "open_chromatin_region", "DNaseI_hypersensitive_site" and "topologically_associated_domain". See the Data Source or Regions Search page for data types available for each species.

Query for faang:

• Gene ID    Overlapping Histone Modification Marks
• Chromatin State Bioproject ID    Specimen and Analysis Tags
• Organism    All FAANG Experiments
• Histone Modification Mark ID    All Overlapping Features
• Organism    FAANG ChIP-seq Experiments
• Organism    FAANG Analyses
• Histone Modification Mark ID    Gene
• Pooled BioSample ID    Component BioSamples

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Most protein information is from UniProt and InterPro. NCBI (RefSeq) and Ensembl protein ids and sequences are also available.

Query for proteins:

• Gene    Protein (UniProt) and Protein Domains
• Transcript ID -> Protein
• Protein    GO Terms
• Organism    Proteins (UniProt) and Publications.
• Gene    Proteins (UniProt)
• Organism    All proteins
• Protein    Gene
• InterPro Name    Protein domains and families

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Homologue datasets include Ensembl Compara and OrthoDB. Ensembl Compara comprises of pairwise relationships with the types "ortholog_one2one", "ortholog_one2many" and "ortholog_many2many". OrthoDB provides clusters of orthologous groups, with cluster ids available as output. Each pairwise relationship in OrthoDB is of the type "orthologue" or "paralogue" (for same-species homologues). The relationships classified as orthologues include in-paralogues.

Query for homology:

• Gene    Homologues
• Gene    Human Homologues    Human Pathways
• Gene    Homologues    Pathways
• Gene    Human Orthologues
• Gene    Homologues for report page

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Gene Ontology annotation is from UniProt. Pathway datasets are from KEGG and Reactome. Interaction data is from BioGRID and IntACT. See the Data Source page the data sets available for each species availability.

Query for function:

• Gene    GO terms
• Gene    Pathway
• Gene    Human Homologues    Human Pathways
• Gene    Interacting genes
• Gene    Homologues    Pathways
• GO Term    Genes
• Protein    GO Terms
• Gene    Reactome Pathway

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Variation data includes variant and variant effects from Ensembl for B. taurus, C. hircus, E. caballus, G. gallus and S. scrofa, variants from EVA for O. aries, and QTL from AnimalQTLdb for B. taurus, C. hircus, E. caballus, G. gallus, O. aries and S. scrofa. Primary identifiers for SNP are rs IDs. Identifiers from SNP arrays are available as alias identifiers. You can convert alias IDs to rs IDs using a query template.

Query for variation:

• SNP Alias ID    dbSNP rsID
• Organism    All QTL
• QTL    Genes
• Trait    QTL
• QTL ID    SNV ID
• Gene ID    Variant Consequences
• SNV rsID    Chromosome Location
• Trait    QTL id    Chromosomal Location

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These template queries allow retrieval of an entire dataset for a specified organism or gene set.

Query for entire gene set:

• Organism    All QTL
• Gene Source and Organism    Gene IDs
• Genome Assembly    Chromosome IDs and Lengths
• Organism    Proteins (UniProt) and Publications.
• Organism    Transcripts + Genes + Database Cross Reference IDs
• Organism    Genes + mRNA + Protein
• Organism    All proteins
• Gene Source and Organism    Genes and Database Cross Reference IDs

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These template queries enable the retrieval of database cross references ids and aliases. Cross references are provided for gene ids across different gene sets (RefSeq and Ensembl). Aliases are provided for SNP ids.

Query for alias and dbxref:

• SNP Alias ID    dbSNP rsID
• Gene ID    Database Cross Reference ID (e.g RefSeq to Ensembl)
• Gene    Cross References
• Organism    Transcripts + Genes + Database Cross Reference IDs
• SNV (rsID)    SNV Alias IDs
• Gene Source and Organism    Genes and Database Cross Reference IDs

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