v32.0
An integrated database for Drosophila and Anopheles genomics
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If you create a MyMine account and log in you can create your own Template Queries.
For a specified KEGG, REACTOME or FlyReactome pathway, list all the genes that are involved for a particular organism
For a certain D. melanogaster gene, show the results from the BDGP in situ project. (Data Source: BDGP).
For a specified organism, show the chromosomal location and sequence length for all genes.
Show the Pathway identifier(s) and name for the selected gene. (Data Source: KEGG, REACTOME or FlyReactome).
Search for GO annotations for a particular gene.
For a specified gene show the known physical and genetic interactions.(Datasources - IntAct & BioGrid).
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*.
Show the proteins for a particular gene.
For a given D. melanogaster gene, show expression data from FlyAtlas.
Show GO terms applied to orthologues of a specific gene. (Data Source: InParanoid, TreeFam, Drosophila Consortium, GO Consortium).
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 genes located on a particular chromosome.
For specified Affymetrix probeset(s) show the corresponding gene. (Data Source: Ensembl).
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 all genes from a particular organism that code for a certain InterPro protein. (InterPro data are available for D. melanogaster, A. gambiae, C. elegans). (Data Source: UniProt).
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).
Show all known interactions between two specific genes. (Data Source: IntAct, BioGrid).
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 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 the chromosome and the chromosome location of a particular gene.
For specified transcription factor(s) show the genes associated binding sites
For a particular Drosophila gene or list of genes show the orthologues in the other Drosophila species.
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, enhancers from FlyBase and predicted sites from Tiffin. (Data Source: REDfly, Tiffin, FlyBase).
Show genes from a particular organism annotated with a particular GO term with a particular evidence code.
For a specific gene, show its protein(s) and the domains found in the protein(s). (Data Source: InterPro).
Show affymetrix probes for a particular gene. (Data Source: Ensembl).
Show gene expression in the following tissue from D. melanogaster and the Affymetrix probes that were used to obtain these data.(Data Source: FlyAtlas).
For a specific protein, show the corresponding gene and its known interactions. (Data Source: IntAct, BioGRID).
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).
List all D. melanogaster genes that are associated with a certain GO term and that have been found to interact with a specific gene. (Data Source: GO, BioGRID, IntAct).
Show the GO terms for all genes in a particular organism which have an orthologue in another organism.
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 the FlyAtlas results and the GO terms applied to the gene.
Search for genes whose proteins have regions for which there is a predicted 3-D structure. Give the location of the region on the protein and the structure details. Data available for D. melanogaster and A. gambiae.
Show the GO annotations for a protein or proteins from a specifc GO ontology (cellular_component, molecular_function, biological_process).
Show the gene that codes for the following protein, with its chromosomal location and length.
For a particular gene, list the transcripts, exons and introns with their chromosomal locations and lengths.
For a particular gene show its interacting genes and their orthologues. (Data Source: IntAct, BioGRID, InParanoid, Drosophila Consortium).
Search for protein domains and families by name. (Data Source: UniProt).
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).
For a specified D. melanogaster gene, show all results from the FlyFISH and the BDGP in situ projects. (Data Source: BDGP, FlyFISH).
Show the set of high-confidence interactions from the Giot et al dataset (or filter this dataset on confidence score). (DataSource:IntAct).
Show all the proteins from a particular organism.
For a particular gene or list of genes give the protein and any PFam domains for that protein.
For a given Gene (or List of Genes) in named organism (default: D. melanogaster) returns the orthologues in a different organisms (default : C. elegans). [keywords: homologue, homolog, paralogue, paralogue, ortholog]
Show all 3' UTRs for a particular organism.
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 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 given D. melanogaster gene, show expression data for a particular tissue from FlyAtlas.(Data Source: FlyAtlas).
Show the genes located between two points on a chromosome. (Data Source: FlyBase, Ensembl).
For a specific published RNAi screen from the DRSC, find all genes that were found to be a certain result in that screen. Result types can be: not screened, not a hit, weak, medium or strong hit. (Data Source: DRSC).
Show the transcript identifiers for a particular gene and the transcript identifiers of its predicted orthologues. (Data Source: InParanoid, Drosophila Consortium).
For a specific D. melanogaster gene, find cis-regulatory modules with overlapping TF Binding sites. Show their locations. (Data Source: REDfly).
For a particular chromosome, show genes that have an insertion. Show the coordinates of each gene and each insertion. (Data Source: FlyBase).
For a particular gene, list the introns with their intron chromosomal locations and lengths.
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.
Show the C. elegans orthologue and RNAi phenotypes for all genes from a particular organism. (Data Source: InParanoid, TreeFam, WormBase).
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.
Search for RNAi phenotypes for a specific C. elegans gene.
For a specified gene show any microRNA genes that are known to target it. (DataSet: miRBase).
For a particular Drosophila gene, search for overlapping insertions. (Data Source: FlyBase).
For a specified organism and chromosomal location show all genes, transcripts and exons.
For a specified organism, show the pairs of physically interacting genes and the corresponding pair of orthologues in another organism. (Data sources: BioGrid, IntAct, InParanoid)
For a specified Enzyme Commission (EC)number show the corresponding genes and proteins in a particular organism.
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 (note: this column also contains the primary assignment).
Show results for RNAi screens for a particular D. melanogaster gene and show its C. elegans orthologues which also have RNAi phenotype data.
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).
For a particular gene or set of genes, give the downstream adjacent gene and any FlyAtlas data that satisfies certain constraints.
For a specific protein, show its 3-D structure and the experimental method used to determine it.
Show the genes, transcripts and INDAC oligos located in a particular chromosome location.
Show all D. melanogaster genes that have been annotated with a particular GO term and that have insertions. (Data Source: GO, FlyBase).
Show all the genes for a specified organism.
For a specific gene, show its exons with their chromosomal locations and lengths.
For a particular protein, show the C. elegans orthologues and their RNAi phenotypes. (Data Source: InParanoid, WormBase).
For a particular gene, find the upstream and the downstream adjacent genes.
For a specified chromosome show all intergenic regions with their chromosomal locations and lengths. (Data Source: FlyMine).
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.
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.
For a particular gene show the transposon insertions that overlap its exons. (Data Source: FlyBase).
Show the GO terms for all genes from a specified organism.
For a certain gene from Drosophila melanogaster, show the mRNA embryonic localisation results from FlyFish.
Find all D. melanogaster gene alleles from a certain allele type. List the corresponding genes. (Data Source: FlyBase).
For a particular pathway (from KEGG, REACTOME or FlyReactome), show all the D. melanogaster genes involved, the orthologous genes in A. gambiae and EST clusters overlapping these genes.
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).
For specified transcript(s) show the corresponding INDAC microarray long oligo, along with its tm, length and sequence.
For the selected organism retrieve all genes and their coding sequences, suitable for export as GFF3 or FASTA.
Show the expression data of the following probeset in the FlyAtlas experiments. (Data Source: Affymetrix, FlyAtlas).
Show all 5' UTRs for a particular organism.
Find RNAi screen results from the DRSC for a particular amplicon, optionally constrain to a particular screen or by the strength of the hit. Result types can be: not screened, not a hit, weak, medium or strong hit. (Data Source: DRSC).
Show all interactions from a specified publication. (Note: you need to enter a pubmed id). Data available for D. melanogaster, C. elegans and S. cerevisiae. (Data Source: BioGRID, IntAct).
For a particular transcription factor binding site from REDfly, give the gene, factor, chromosomal location, sequence and pubmed id. (Data Source: REDfly).
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 particular A. gambiae gene, show its expression according to the data of Koutsos et al at a particular developmental stage. This template allows you to query on the general stage: use LIKE embryo; larva; pupa; adult female; adult male; or adult. The templates Gene [A. gambiae] -> Life cycle expression data (filter on specific stage (and ratio)) allow you to filter on more specific stages. Note that the reference sample in this experiment is pooled RNA produced in vitro from ESTs that were used as substrates to produce amplicons for the spotted microarrays.
For a particular organism show the natural transposable elements and their chromosomal insertion sites.
For a particular gene, search for the C. elegans orthologue and its RNAi phenotype. (Data Source: InParanoid, WormBase).
For a particular INDAC long oligo, search for corresponding D. melanoster genes and show their chromosomal coordinates.
For a particular gene, search for overlapping genes.
For a particular transposable element show the individual elements and their chromosomal locations.
For a specific published RNAi screen from the DRSC, find all genes that were found to be a certain result in that screen and that have alleles. Result types can be: not screened, not a hit, weak, medium or strong hit.(Data Source:DRSC, FlyBase).
For a specified organism, show all pairs of physically interacting genes whose orthologues or inParalogues (co-orthologues) are also been shown to physically interact. (Data Sources: Biogrid, IntAct, Treefam, Inparanoid).
Show all miRNA for a specified organism.
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).
Find all D. melanogaster genes interrupted by a specific DrosDel deletion. Show the chromosomal locations of the deletion and the genes. (Data Source: FlyBase).
For a cDNA clone or list of clones give the corresponding gene identifiers.
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).
For a specific gene from D. melanogaster, show its Cis-Regulatory Modules, their chromosomal locations and lengths. (Data Source: REDfly)
Search for RNAi phenotypes for a particular C. elegans gene and show the predicted orthologues for this gene. (Data Source: WormBase, InParanoid, Drosophila Consortium).
For a particular Drosophila gene, search for corresponding INDAC long oligos.
For a particular EST clone show the chromosome location of the cluster to which it belongs and the gene which maps to this location. (Data Source: VectorBase).
For a particular organism list the natural transposable elements.
For a particular A. gambiae EST cluster show its ESTs and the chromosomal location of the cluster. (Data Source: VectorBase).
Search for C. elegans genes with a particular RNAi phenotype.
Show all the Cis-Regulatory Modules from REDfly that have been associated with a specific anatomy ontology term. (Data Source: REDfly).
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 particular D. melanogaster gene, search for overlapping point mutations with their chromosomal coordinates. (Data Source: FlyBase).
For a particular EST clone from A. gambiae show the clusters it belongs to and the chromosomal locations. (Data Source: VectorBase).
Search for C. elegans genes with a specific RNAi phenotype and show the orthologues of these genes. (Data Source: WormBase, InParanoid).
For a particular chromosomal location from A. gambiae show all EST clusters and ESTs. (Data Source: VectorBase).
Show all 3-D protein structures that have been determined using a certain experimental method. Data available for D. melanogaster (Data Source: PDB).
Show the chromosomal location of all Anopheles gambiae EST clusters and ESTs of a particular type. Use TCLAG* to show all T-clusters (type 1 EST-to-genome alignments). These are defined as those clusters which contain at least one unambiguously mapped EST. Use NCLAG* to show clusters with no type 1 matches.
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 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).
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 specific chromosomal location of D. melanogaster, show all Cis-Regulatory Modules from REDfly with their length and chromosomal coordinates. (Data Source:REDfly).
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).
Show all A. gambiae clusters which have no match to the genome. (Data Source: VectorBase).
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).
Find all D. melanogaster gene alleles created in a certain way. Give the corresponding gene for the allele. (Data Source: FlyBase).
Show all transposable element insertion sites for a particular organism.
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).
