vv53 February 2022
An integrated database for Drosophila genomics
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Search for GO annotations for a particular gene.
Show the Pathway identifier(s) and name for the selected gene.
Show genes located on a particular chromosome.
For specified D. melanogaster transcription factor(s), show the binding sites, chromosomal locations, genes where the sites are located and give the sequence of the binding site, if any. (Data Source: Redfly).
Find all genes that are associated with a particular GO term in a specific organism. This template will return genes that have been assigned the given GO term as well as genes that have a more specific GO term.
Show all known transcription factors for a particular D. melanogaster gene. (Data Source: REDfly, FlyBase).
Show all known regulatory elements for a particular D. melanogaster gene. Regulatory elements can include: CRMs and TF binding sites from REDfly and enhancers from FlyBase. (Data Source: REDfly, FlyBase).
For a certain D. melanogaster gene, show the results from the BDGP in situ project. (Data Source: BDGP).
Show gene expression in the following tissue from D. melanogaster and the Affymetrix probes that were used to obtain these data.(Data Source: FlyAtlas).
Show the chromosome and the chromosome location of a particular gene.
For specified transcription factor(s) show the genes associated binding sites
For a given D. melanogaster gene, show expression data from FlyAtlas.
For a specified gene, show physical and genetic interaction partners. Optionally constrain to show just physical or genetic interactions or interactions determined by a specific method.
For a given Gene (or List of Genes) in named organism (default: D. melanogaster) returns the orthologues and the sequence of the gene(s) and orthologous genes. Optionally constrain the organism for which orthologues are shown and the data source from which the orthologue predictions are derived. Currently orthologue predictions are available from TreeFam, Panther and the Drosophila 12 genomes project. [keywords: homologue, homolog, paralogue, paralogue, ortholog]
For a specified gene or set of genes show the RNA_seq expression levels. Optionally constrain your search to genes with a particular expression level or score and/or show expression at a particular developmental stage. Data source: modENCODE RNA_seq data analysed by FlyBAse. Note: The expression scores are binned into the expression levels as follows: No/Extremely low expression: 0-0; Very low expression: 1-3; Low expression: 4-10; Moderate expression: 11-25; Moderately high expression: 26-50; High expression: 51-100; Very high expression: 101-1000; Extremely high expression: >1000;
For a given Gene (or List of Genes) in named organism (default: D. melanogaster) returns the orthologues. Optionally constrain the organism for which orthologues are shown and the data source from which the orthologue predictions are derived. Currently orthologue predictions are available from TreeFam, Panther and the Drosophila 12 genomes project. [keywords: homologue, homolog, paralogue, paralogue, ortholog]
For a particular Drosophila gene show results from Arbeitman et al (2002) microarray time course expression. Optionally constrain by a specific stage and filter on the median signal ratio. Note that the reference sample in this experiment is pooled mRNA representing all stages of the life cycle. To query general stages change = to LIKE and enter e.g. *Embryo* or *Adult*.
For a particular gene, list the transcripts, exons and introns with their chromosomal locations and lengths.
Show all the genes for a specified organism.
Show the gene that codes for the following protein, with its chromosomal location and length.
Show the GO terms for all genes from a specified organism.
For a particular gene, show any regulatory elements found in its upstream intergenic region and the chromosome location of these regions. Regulatory elements can include: CRMs and TF binding sites from REDfly and enhancers from FlyBase. (Data Source: REDfly, FlyBase).
Find all D. melanogaster alleles that have a phenotype in a specific anatomical structure and that are from a certain allele class. (Data Source: FlyBase)
For a specified gene or gene list, show any interactions with genes involved in a specified pathway.
Show the human genes associated with a specified disease and their orthologues. Optionally constrain the organism for which orthologues are shown.
Show RNAi phenotypes for a specified gene or genes.
Show gene expression data for a particular developmental stage according to the Arbeitman et al data set and filter this data on the median signal ratio. This template allows you to query on the general stage: use LIKE *Embryo*; *Larvae*; *Metamorphosis*; *Adult female* or *Adult male*. The templates Microarray Time course data from Arbeitman et al (filter on specific stage (and ratio)) --> Genes [D. melanogaster], allow you to filter on more specific stages. Note that the reference sample in this experiment is pooled mRNA representing all stages of the life cycle.
Show the GO terms for all genes in a particular organism which have an orthologue in another organism.
For a given gene or set of genes show orthologous human genes which have an associated OMIM disease. Optionally constrain the search to use a particular orthologue mapping (Ensembl Compara or TreeFam).
For a specified protein, show physical and genetic interaction partners. Optionally constrain to show just physical or genetic interactions or interactions determined by a specific method.
For a particular organism, show all intergenic regions with their chromosomal locations, lenghts and adjacent genes. (Data Source: FlyMine).
For a given D. melanogaster gene, show expression data for a particular tissue from FlyAtlas.(Data Source: FlyAtlas).
For specified miRNA(s), find all predicted target transcripts and their genes. Show the location of the target sites, the score for each site and the p-value. (Data Source: miRBase).
Show all the proteins from a particular organism.
For a specified ImaGo term and/or stage range, show all the D. melanogaster genes that are associated with it according to the BDGP in situ project. (Data Source: BDGP).
Show phenotypes for genes identified in a specified RNAi screen.
For a specified gene show any microRNA genes that are known to target it. (DataSet: miRBase).
For a given Gene A (or List A of Genes) show any interactions that occur with gene B (or List B of Genes)
Given a gene show the associated GO terms, and all parents to the top of the directed graph. The query returns a column containing the assigned GO term and a column containing all parents of that primary assignment.
Show all alleles for a specific Drosophila gene. Show all available information, eg mutagen, allele class and phenotype linked to each allele. (Data Source: FlyBase)
For a specified KEGG, REACTOME or FlyReactome pathway, list all the genes that are involved for a particular organism
For the selected organism retrieve all genes and their coding sequences, suitable for export as GFF3 or FASTA.
Returns a list of publications that reference a specified gene. References are loaded from FlyBase for all Drosophila species, and from NCBI for D. melanogaster, C. elegans and S. cerevisiae.
Show genes expressed in a set of FlyAtlas tissues.
Show the proteins for a particular gene
Show the genes located between two points on a chromosome. (Data Source: FlyBase, Ensembl).
Show affymetrix probes for a particular gene. (Data Source: Ensembl).
Show genes expressed in a set of tissues/stages according to the modENCODE RNA_seq data. The expression scores are binned into the expression levels as follows: No/Extremely low expression: 0-0; Very low expression: 1-3; Low expression: 4-10; Moderate expression: 11-25; Moderately high expression: 26-50; High expression: 51-100; Very high expression: 101-1000; Extremely high expression: >1000;
For a particular transcription factor binding site from REDfly, give the gene, factor, chromosomal location, sequence and pubmed id. (Data Source: REDfly).
For a particular gene, find the upstream and the downstream adjacent genes.
Show all the genes known to be involved in a specific KEGG, REACTOME or FlyReactome pathway and their orthologous genes in one specific organism. (Data Source: KEGG, Reactome, FlyReactome, inParanoid, Drosophila consortium).
Show all regulatory elements in a particular chromosomal location in the D. melanogaster genome. Regulatory elements can include: CRMs and TF binding sites from REDfly, enhancers from FlyBase and predicted sites from Tiffin. (Data Source: REDfly, FlyBase, Tiffin).
Show the human genes associated with a specified disease.
For a particular gene, list the introns with their intron chromosomal locations and lengths. To show introns for all genes, turn off the constraint on the gene name.
Show RNA_seq expression data for all genes at a specified developmental stage. Optionally also filter on expression level or expression score. Data source: modENCODE RNA_seq data analysed by FlyBase. Note: The expression scores are binned into the expression levels as follows: No/Extremely low expression: 0-0; Very low expression: 1-3; Low expression: 4-10; Moderate expression: 11-25; Moderately high expression: 26-50; High expression: 51-100; Very high expression: 101-1000; Extremely high expression: >1000;
For a specified organism and chromosomal location show all genes, transcripts and exons.NOTE THAT THE LOCATION SHOWN IS THE LOCATION OF THE EXON.
Show the transcript identifiers for a particular gene and the transcript identifiers of its predicted orthologues. (Data Source: InParanoid, Drosophila Consortium).
For a given embryonic stage of Drosophila melanogaster, show which genes are expressed or not expressed according to the FlyFish and BDGP in situ projects.
Show the GO annotations for a protein or proteins from a specifc GO ontology (cellular_component, molecular_function, biological_process).
For a specified organism, show the chromosomal location and sequence length for all genes.
For a specified D. melanogaster gene, show all results from the FlyFISH and the BDGP in situ projects. (Data Source: BDGP, FlyFISH).
Search for protein domains and families by name. (Data Source: UniProt).
Show the publications for each gene in one organism. References are loaded from FlyBase for all Drosophila species, and from NCBI for D. melanogaster, C. elegans and S. cerevisiae.
For a specified gene or list of genes show the alleles and the stocks available. Optionally, you can filter the search with a specific allele of the gene and/or show only those stocks available from a specified stock centre.
For specified Affymetrix probeset(s) show the corresponding gene. (Data Source: Ensembl).
Show all 3' UTRs for a particular organism.
Show all genes that were mentioned in a specific publication. References are loaded from FlyBase for all Drosophila species, and from NCBI for D. melanogaster, C. elegans and S. cerevisiae.
For a specific gene, show its exons with their chromosomal locations and lengths. To show exons for all genes, turn off the constraint on the gene name.
Show proteins and corresponding genes which have a specified protein domain or family.
For a particular D. melanogaster chromosomal location, show all REDfly TF binding sites with their locations and associated genes and transcription factors. (Data Source: REDfly).
For a particular D. melanogaster gene, search for overlapping point mutations with their chromosomal coordinates. (Data Source: FlyBase).
For a given Gene A (or List A of Genes) show any associated Pathway(s) in common with Gene B (or List B of Genes). Datasource: KEGG or REACTOME. Keywords: pathways, cascade, metabolism, reaction
Show the genes, transcripts and INDAC oligos located in a particular chromosome location.
For a particular Drosophila gene, search for overlapping insertions. (Data Source: FlyBase).
For a specific gene from D. melanogaster, show its Cis-Regulatory Modules, their chromosomal locations and lengths. (Data Source: REDfly)
For a particular gene, search for overlapping genes.
For a specified Enzyme Commission (EC)number show the corresponding genes and proteins in a particular organism.
For a specified GO term (and children of this term) find all the genes in a particular organism that have an orthologue in another organism
For a certain gene from Drosophila melanogaster, show the mRNA embryonic localisation results from FlyFish.
Show all miRNA for a specified organism.
For a particular chromosome, show genes that have an insertion. Show the coordinates of each gene and each insertion. (Data Source: FlyBase). NOTE: Can be slow to run.
For a specific chromosomal location of D. melanogaster, show all CRMs and the TF binding sites that overlap these CRMs, according to REDfly. Show the chromosomal positions and lengths of all CRMs and TF binding sites.
For a certain embryonic stage of D. melanogaster and a given expression term, show all the genes that are expressed according to the FlyFISH project.
Show the CDS and its sequence for all genes from a particular organism. This template contains an additional constraint to limit the result to one CDS per sequence (e.g all -PA CDS from D. melanogaster).
Show all the binding sites for the transcription factors according to the REDfly dataset.
Show all D. melanogaster genes that have been annotated with a particular GO term and the DrosDel deletions which would delete these genes. Show whether the deletion is available. (Data Source: GO, FlyBase, DrosDel).
Show protein domain information for the proteins of a specified gene.
Show all D. melanogaster genes that have been annotated with a particular GO term and that have insertions. (Data Source: GO, FlyBase).
Show the expression data of the following probeset in the FlyAtlas experiments. (Data Source: Affymetrix, FlyAtlas).
Show all 5' UTRs for a particular organism.
For a particular Drosophila, list the genes, transcripts, exons and introns with their chromosomal locations and lengths.
For a particular gene or set of genes, give the downstream adjacent gene and any FlyAtlas data that satisfies certain constraints.
This search returns the publications referenced by Uniprot in their annotation of the protein. It does not provide a comprehensive list of publications for the protein(s).
For a specific chromosome from D. melanogaster, show all CRMs with insertions. Show the chromosomal locations for each CRM and each insertion. (Data Source: REDfly, FlyBase).
For a particular gene show the transposon insertions that overlap its exons. (Data Source: FlyBase).
For a particular gene, find the upstream and the downstream adjacent genes and their chromosome locations.
Show all transposable element insertion sites for a particular organism.
Show all the Cis-Regulatory Modules from REDfly that have been associated with a specific anatomy ontology term. (Data Source: REDfly).
For a specified chromosome show all intergenic regions with their chromosomal locations and lengths. (Data Source: FlyMine).
For a cDNA clone or list of clones give the corresponding gene identifiers.
For a particular INDAC long oligo, search for corresponding D. melanoster genes and show their chromosomal coordinates.
Show protein domains and families for a specified protein.
For a particular gene or set of genes, give the upstream adjacent gene and FlyAtlas data that satisifies certain constraints. (Note: the FlyAtlas data is for the adjacent gene).
Show all D. melanogaster genes that have been annotated with a particular GO term and the point mutations which overlap these genes. (Data Source: GO Consortium, FlyBase).
For a specified Intron or set of introns, return any overlapping regulatory regions.
For a particular organism show the natural transposable elements and their chromosomal insertion sites.
For specified transcript(s) show the corresponding INDAC microarray long oligo, along with its tm, length and sequence.
For the following intergenic region from D. melanogaster, show all regulatory elements with their chromosomal locations and lengths. Regulatory elements can include: CRMs and TF binding sites from REDfly, enhancers from FlyBase and predicted sites from Tiffin. (Data Source: FlyBase, REDfly, Tiffin).
For a specified organism return the sequence of all genes. Can be used to output a Fasta file of all sequences for use with programs such as BLAST.
Find all D. melanogaster genes interrupted by a specific DrosDel deletion. Show the chromosomal locations of the deletion and the genes. (Data Source: FlyBase).
Find all D. melanogaster gene alleles created in a certain way. Give the corresponding gene for the allele. (Data Source: FlyBase).
For a particular transposable element show the individual elements and their chromosomal locations.
Show alleles in which mutations cause a specific type of phenotype, such as enhancer or suppressor.
For a particular point mutation in D. melanogaster, search for overlapping genes. Show chromosomal coordinates for the point mutation and the genes. (Data Source: FlyBase).
For a particular Drosophila gene, search for corresponding INDAC long oligos.
Find all D. melanogaster gene alleles from a certain allele type. List the corresponding genes. (Data Source: FlyBase).
For a particular organism list the natural transposable elements.
For a specific chromosomal location of D. melanogaster, show all Cis-Regulatory Modules from REDfly with their length and chromosomal coordinates. (Data Source:REDfly).
Show all known enhancer elements for a particular D. melanogaster gene. (Data Source: FlyBase).
For given MeSH term show all publications.
This search returns the publications referenced by Uniprot AND the publications for the Gene. This gives two columns of pubmed Ids: the first for the publications from Uniprot and the second for the publications for the Gene. To create a single list of all publications, create a list for the first set and then add the second set to this list using the functions under 'Create/Add to list'.
For a specified CRM, show all associated anatomy terms. (Data Source: REDfly).
For specified protein (or list of proteins) return the protein domains and the GO annotation assigned to each domain.
