A data warehouse for the modENCODE project
Show binding sites for a gene or list of genes. This template will only show binding sites overlapping the gene. By default all binding sites will be returned. Use the optional constraints if you want to return specific binding sites, eg for a specific transcription factor or histone modification. Additionally use the optional constraints to further filter by developmental stage, strain, cell line or tissue. Please note that to filter for C. elegans transcription factors there is a separate constraint option.
Show expression levels for exons associated with given genes.
Show the binding sites for a particular chIP target in the upstream or downstream flanking region of a specified gene or genes.
Show binding sites identified for a particular transcription factor or list of transcription factors.
Show genes which have binding sites in their upstream flanking region for a particular TF.
Show chIP binding sites identified for a particular target gene or protein. Keywords: Transcription factors, Histone modification, Modified histone protein, Chromatin proteins, ChIP, Antibody target.
For selected modENCODE experiments find features that were generated under certain experimental conditions, for example by constraining the cell line, developmental stage or antibody name. You can choose more than one experiment by control clicking in the box.
Show the Pathway identifier(s) and name for the selected gene. (Data Source: REACTOME or FlyReactome).
For a specified REACTOME or FlyReactome pathway, list all the genes that are involved for a particular organism
For a particular histone modification show all the binding sites identified at all developmental stages.
Gene expression scores by developmental stage from the experiment modENCODE_3305
Show all the genes for a particular organism.
Displays cross references among modENCODE and other public repositories
Gene expression scores by cell line from the experiment modENCODE_3305
Show all submissions for a specified chIP target.
Show all submissions for a particular experiment type.
Show all 3' UTRs for a particular organism. NOTE: you can restrict it to show only the 3'UTRs identified by the genome projects using the optional filter provided.
For a specified gene or list of genes show the locations of a specific gene feature. Feature types include Sl1_acceptor_site, Sl2_acceptor_site, polyA_site, polyA_signal_sequence, exon, exon_region, three_prime_UTR/RST or UST, five_prime_UTR/RST or UST, stop_codon, transcript, transcript_region, mature_transcript, intron, transcription_end_site, EST, overlapping_EST_set, TSS, intron, binding_site. To return all feature types, turn off the feature type (SO Term -> Name) constraint - once you have your results table you can then view the number of each type of feature using the feature type column summary button. Keywords: Gene structure; Gene features.
Show GO terms applied to orthologues of a specific gene.
Search for GO annotations for a particular gene.
Show all transcript regions identified in a particular tissue on a specified chromosome.
Show all binding sites within a specified chromosome location at a particular developmental stage.
For a particular list of submissions show the binding sites found within a specified chromosome location at a specified developmental stage.
Show transcript regions and their overlapping genes identified in a particular cell line.
Show transcript regions identified for a particular gene or list of genes.
For a particular gene or list of genes, show the 3'UTR(s) identified by the modENCODE project.
Show transcript regions identified in a particular tissue at a specified chromosome location and the genes which overlap the transcript.
For a specific gene, show its exons and their chromosomal locations and lengths.
For a specific gene, show features of a specified type that have been mapped in the gene(s) flanking regions. Features can be shown just for the flanking region or the gene itself can also be included.
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 particular gene, list the transcripts, introns and exons and show the chromosomal locations and lengths of the transcripts and exons.
For a given gene, give all its transcripts with their respective lengths. For each transcript, give its translation with its respective length.
Fly exon expression score by developmental stage from the experiment modENCODE_3305
Show all 5' UTRs for a particular organism. NOTE: to restrict the result to shows 5'UTRs identified by the genome projects only please enable the constraint in the form.
Displays data used in the submission and references to other public repositories
For a particular submission (or list of submissions), or experiment, or project show the binding sites identified and any adjacent genes at a specified distance. (NOTE: upstream/downstream refers to position relative to the genes not the binding sites).
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).
Show the predicted orthologues between two organisms.
Returns a list of publications that reference a selected gene
Show all origins of replication identified in a particular cell line at a particular chromosome location.
For a particular gene, find the upstream and the downstream adjacent genes.
Show genes located on a particular chromosome.
Show the cell lines used for a particular experiment type in a specified organism.
Show regions of copy number variation identified in a particular tissue (currently 16C follicle cells or Salivary gland). Optionally constrain your results to a chromosome or chromosome region.
Display sample characteristics for submissions of a given experiment
Show binding sites that overlap origins of replication on a particular chromosome. The binding sites are constrained by submission, so it is possible to limit the query to a particular type of binding site, e.g. histone binding sites, by the submission or list of submissions.
Show the proteins for a particular gene.
submissions with their experimental factors
Show submissions which have used a particular array.
to find results files using various selection criteria
For a particular submission or list of submissions show all the binding sites identified within a certain chromosome location, or developemtal stage.
Show the chromosomal location and the length of the gene that codes for the following protein.
All submissions with a given protocol type
Show all genes from a particular organism that code for proteins with a certain protein domain.
Fly exon expression score by cell line from the experiment modENCODE_3305
Show the transcript identifiers for a particular gene and the transcript identifiers of its predicted orthologues.
Show all features and their chromosome location for a particular project.
Find all D. melanogaster gene alleles created in a certain way. Give the corresponding gene for the allele. (Data Source: FlyBase).
retrieves all submissions associated with a given assay factor.
Show all submissions which have mapped features of a specified type.
For a particular chromosome show start, end and length of all intergenic regions.
© 2002 - 2013 Department of Genetics, University of Cambridge, Downing Street,
Cambridge CB2 3EH, United Kingdom