A data warehouse for the modENCODE project
Show the chromosomal location and sequence for all genes from a particular organism.
Show the publications for each gene in an organism. Data currently available for D.melanogaster.
Show the predicted orthologues between two organisms.
Show the genes, transcripts and exons located between two points on a chromosome. Give the location of the exons.
Show the genes located between two points on a chromosome
Show genes located on a particular chromosome.
For a particular chromosome show start, end and length of all intergenic regions.
Give the GO term name for a particular GO term identifier.
Find the GO primaryIdentifier for a specific term.
Search for genes in one specific organism that have been associated with a particular GO annotation. Only genes that are associated with this actual GO term will be returned. Genes which have this term as a parent of their actual GO term will not be returned.
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.
For a particular gene, find the upstream and the downstream adjacent genes.
For a particular gene show its chromsomal location.
For a specific gene, show its exons and their chromosomal locations and lengths.
Given a gene show the associated GO terms, and the all parents to the top of the directed graph. If 'isPrimaryAssignment' is 'true' then that GO term was actually assigned to the gene. Likewise if it is false then the GO term is some more general parent term.
Search for GO annotations for a particular gene.
Show all primary identifiers for a gene, given an identifier.
For a particular gene, list the introns and show the intron chromosomal locations and lengths.
Show GO terms applied to orthologues of a specific gene.
For a particular gene, show predicted orthologues in one particular organism.
Show predicted orthologues for a particular gene.
For a particular gene, search for overlapping genes.
For a particular gene show the point mutations that overlap its exons.
Show the proteins for a particular gene.
Show the transcript identifiers for a particular gene and the transcript identifiers of its predicted orthologues.
Show the predicted transcripts and the number of exons for each transcript for a particular gene.
For a particular gene, list the transcripts and exons and show the chromosomal locations and lengths of the transcripts and exons.
For a particular gene, show its transcripts and introns and their chromosomal locations and lengths.
For a particular gene, show all transcripts, exons and introns.
For a particular gene show the length and chromosomal location of the upstream intergenic region.
Returns a list of publications that reference a selected gene
For a given gene, give all its transcripts with their respective lengths. For each transcript, give its translation with its respective length.
For a particular gene, search for overlapping point mutations. Show the chromosome coordinates of any point mutations.
For a particular gene show the transposable element insertion sites that overlap its exons.
For a particular gene, search for overlapping transposable element insertion sites.
For the following gene symbol, show its gene primaryIdentifier
For a particular gene or set of genes and a particular GO term, show which gene(s) have the GO term given.
Search for protein domains and families by name.
Show genes from a particular organism annotated with a particular GO term.
Show genes from a particular organism annotated with a particular GO term with a particular evidence code.
Show genes from a particular organism annotated with a particular GO term and GO evidence code which also have a 'with' annotation (The 'with' field holds an additional primaryIdentifier for annotations using certain evidence codes)
Show all genes from a particular organism that have been annotated with a particular Go term(s) and the point mutations which overlap these genes.
Show all genes from a particular organism that have been annotated with a particular Go term(s) and the transposable element insertion sites which overlap these genes.
For a particular organism show all genes that have a chromosomal location.
Show all genes from a particular organism that code for proteins with a certain protein domain.
Show all the genes for a particular organism.
For a particular organism, show all intergenic regions.
Show proteins from a particular organism that have a particular protein domain or family.
Show all the proteins from a particular organism.
For a particular organism, show all its transcripts.
For a particular organism, search for any genes with overlapping point mutations. Show chromosome coordinates of genes and point mutations.
For a specific P-element insertion, search for overlapping genes. Show chromosomal coordinates of the insertion and the genes.
For a particular point mutation, search for overlapping genes. Show chromosome coordinates for the genes.
Show all GO terms that have been associated with the gene that codes for the following protein.
Show the chromosomal location and the length of the gene that codes for the following protein.
For a particular protein show the identifiers and symbol of the corresponding gene.
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).
