FlyMine

The gene models and other genome annotation in FlyMine are provided by a variety of source databases including: FlyBase, UniProt, Ensembl and over 30 other data sources. Read more

Query for genes:

• All genes in organism    All chromosomal locations.
• Gene    Proteins.
• Chromosome    All genes.
• Gene    Chromosomal location.
• Gene    Protein + Protein domains
• Organism    All intergenic regions.
• Organism    Genes + Proteins with region with 3-D structure.
• Protein    Gene.

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FlyMine loads physical interactions from IntAct and BioGRID and genetic interactions from FlyBase. Read more

Query for interactions:

• Gene    Interactions
• Gene1 + Gene2    Interactions.
• Protein    Gene + Interactions.
• GO term + Interacting gene [D. melanogaster]    Genes.
• Gene    Interacting genes + Orthologues.
• Dataset [Giot et al]    High confidence protein interactions (filter on confidence value).
• All pairs of interacting proteins in organism 1    Orthologues in organism 2.
• Publication [D. melanogaster]    Interactions.

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FlyMine loads homologue predictions from Ensembl, KEGG and TreeFam. Read more

Query for homology:

• Gene    Orthologues + GO terms of these orthologues.
• Gene [D. melanogaster]    Orthologues in other Drosophila species
• Organism    GO terms + Orthologues in one specific organism.
• Gene    Interacting genes + Orthologues.
• Gene    Orthologues
• Gene    Transcript + Transcripts from orthologues.
• All genes in organism    C. elegans orthologues + RNAi phenotypes of these orthologues.
• All pairs of interacting proteins in organism 1    Orthologues in organism 2.

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FlyMine loads Gene Ontology annotation from MGI, FlyBase, WormBase, UniProt, SGD, and InterPro; domain data from InterPro; disease data from OMIM; and pathways data from Reactome and KEGG. Read more

Query for function:

• Pathway    Genes.
• Gene    Pathway.
• Gene    GO terms.
• Gene    Orthologues + GO terms of these orthologues.
• GO term name [and children of this term]    Genes in one specific organism.
• Affymetrix probeset    Gene.
• Protein Domain    Proteins + Genes coding for these proteins.
• Phenotype [D. melanogaster]    Alleles.

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FlyMine loads transcriptional regulation data from FlyBase and REDFly. Read more

Query for regulation:

• TranscriptionFactor    Genes that have binding sites for this factor.
• Gene [D. melanogaster]    Regulatory elements in the upstream intergenic region.
• Gene [D. melanogaster]    Regulatory elements.
• RNAi Screen + Result type [D. melanogaster]    RNAi Screen results.
• Gene [D. melanogaster]    CRMs + TF binding sites overlapping these CRMs.
• Chromosome [D. melanogaster]    All genes with insertions.
• Gene    microRNA (miRNA) gene
• Gene [D. melanogaster]    RNAi screen results + C. elegans orthologues with RNAi results

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FlyMine loads gene expression data for Drosophila melanogaster and Anopheles gambiae from FlyAtlas, BDGP, ArrayExpress and Fly-FISH. Read more

Query for expression:

• Gene [D. melanogaster]    BDGP in situ data.
• Gene [D. melanogaster]    Microarray Time course expression data from Arbeitman et al.
• Gene [D. melanogaster]    FlyAtlas data.
• Microarray Time course data from Arbeitman et al. (filter on stage and ratio)    Genes [D. melanogaster].
• Tissue [D. melanogaster]    FlyAtlas data.
• Gene [D. melanogaster]    FlyAtlas + GO.
• BDGP    Genes.
• Gene [D. melanogaster]    FlyFish + BDGP in situ data.

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