v 17.1 04June2010
A data warehouse for the modENCODE project
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modMine > Templates ?
For all genes, list the taxonIds available. Used by webservice to construct links to other intermines.
Show the predicted orthologues between two organisms.
Show submissions which have used a particular array.
All Cell Lines used in the modENCODE project
For a particular cell line show the origins of replication identified on a particular chromosome.
Show all origins of replication identified in a particular cell line at a particular chromosome location.
Show all origins of replication identified in a particular cell line.
Show transcript regions and their overlapping genes identified in a particular cell line.
For an antibody target gene from C. elegans show the binding sites that fall upstream or downstream of a gene by a specified distance. (NOTE: currently antibody target genes for C. elegans are modelled slightly differently to D. melanogaster due to experimental differences - hence the template specific to C. elegans).
For a particular antibody target gene and cell line show the binding sites identified. NOTE: This query searches for binding sites for a particular antibody target gene. Some submissions use different antibody names for antibodies with the same target gene. To find all binding sites for a particular antibody use the query 'Antibody + Cell Line --> Binding sites'.
Show binding sites identified within a certain chromosomal region by a particular antibody target gene in a particular cell line. NOTE: This query searches for binding sites identified for a particular antibody target gene. Some submissions use different antibody names for antibodies with the same target gene. To find all binding sites for a particular antibody use the query 'Antibody + Chromosomal location + Cell line --> Binding sites'.
Show binding sites identified within a certain chromosomal region for a particular antibody target gene at a particular developmental stage. NOTE: This query searches for binding sites identified for a particular antibody target gene. Some submissions use different antibody names for antibodies with the same target gene. To find all binding sites for a particular antibody use the query 'Antibody + Chromosomal location + Developmental stage --> Binding sites'.
Show binding sites within a specified chromosome location that were identified using an antibody to a particular target gene. NOTE: This query searches for binding sites for a particular antibody target gene. Some submissions use different antibody names for antibodies with the same target gene. To find all binding sites for a particular antibody use the query 'Antibody + Chromsome location --> Binding sites'.
Show binding sites identified for a particular antibody target gene at a particular developmental stage in a particular cell line. NOTE: This query searches for binding sites for a particular antibody target gene. Some submissions use different antibody names for antibodies with the same target gene. To find all binding sites for a particular antibody use the query 'Antibody + Developmental stage + Cell line --> Binding sites'.
Show binding sites identified using an antibody to a particular target gene at a particular developmental stage.
For a particular antibody target gene and developmental stage show the binding sites that fall upstream or downstream of a gene by a specified distance.
Show all binding sites for a particular antibody target gene.
For an antibody target gene (or list of genes) show the binding sites that fall upstream or downstream of a gene by a specified distance.
For a particular antibody target gene show the binding sites that fall in upstream intergenic regions and the downstream gene.
Show binding sites identified by an antibody to a particular target gene.
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
For a given chromosome show the 3'UTRS and associated genes. NOTE: Only 3'UTRs identified by modENCODE submissions will be shown, not those identified by the organism genome projects.
For a given chromosome show the 5'UTRs and associated genes. NOTE: Only 5'UTRs identified by modENCODE submissions will be shown, not those identified by the organism genome projects.
For a particular chromosome show start, end and length of all intergenic regions.
Show all binding sites within a specified chromosome location at a particular developmental stage.
Show all features identified by the modencode project within a particular chromosome location.
Retrieve submissions with a certain data type and display details
Retrieve all submissions with a certain data type
All the submissions dealing with a given developmental stage
For a particular gene and a particular developmental stage show the introns identified by the C. elegans transriptome project.
Show antibodies which have been used at a particular developmental stage together with their target gene and the submission.
Show transcript regions identified at a particular developmental stage and genes which overlap these regions.
Show all exons identified in the modEncode project which overlap FlyBase exons, on a particular chromosome
For a set of exons from a specified submission or list of submissions, on a particular chromosome, show the FlyBase exons which overlap.
Show all the 3'UTRs and associated genes identified by a particular experiment.
All the submissions for a given experiment name
Show the cell lines used for a particular experiment type in a specified organism.
Show all developmental stages used for a particular experiment type in a specified organism.
Show all submissions for a particular experiment type.
Show the developmental stages for a particular experimental property type. For example, property type can be set to 'array'.
For a feature or a set of features, show overlapping genes.
For a particular set of features on a particular chromosome show the overlapping Flybase genes. Select a list of features from the drop-down menu. The features can be any located sequence feature, e.g. gene, mRNA, exon.
For a particular Gene or list of genes, show overlapping transcript regions identified in a particular cell line.
For a particular gene or list of genes show the transcript regions identified at a particular developmental stage.
For a particular gene or list genes, show transcription factor binding sites in the upstream intergenic region. Specify either a single submission to find binding sites for a specific transcription factor or a list of submissions.
For a particular gene, find the upstream and the downstream adjacent genes.
For a particular gene or list of genes show the binding sites in the upstream intergenic region.
For a particular gene show its chromsomal location.
For a specific gene, show its exons and their chromosomal locations and lengths.
For a gene or list of genes show the features that overlap with in the upstream or downstream flanking regions.
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 or list of genes show the submissions for which data is available for this gene.
Show the transcript identifiers for a particular gene and the transcript identifiers of its predicted orthologues.
Show transcript regions identified for a particular gene or list of genes.
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.
Show introns identified for a particular C. elegans gene from the C. elegans transcriptome project and give their chromosomal location.
For gene models show overlapping genes from FlyBase for a particular chromsome.
For a set of gene models show those which have overlaping cDNA evidence.
For a particular gene or list of genes, show the 3'UTR(s) identified by the modENCODE project.
The list of submissions in modMine
For a particular histone modification show all the binding sites identified at all developmental stages.
Returns organisms with orthologues and their datasets
Search for protein domains and families by name.
to check if a submission is in modMine
you can use either the title or the DCC id.
All the submissions for a given Lab
Show all 3' UTRs for a particular organism. NOTE: this template shows 3'UTRs identified by the genome projects NOT by the modENCODE projects.
Show all 5' UTRs for a particular organism. NOTE: this template shows 5'UTRs identified by the genome projects NOT by the modENCODE projects.
Show all genes from a particular organism that code for proteins with a certain protein domain.
Show all the genes for a particular organism.
Show proteins from a particular organism that have a particular protein domain or family.
For a specified organism show all antibodies, their targets and the cell line used.
For a specified organism show all antibodies, their targets and the developmental stages used.
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.
used for mapping to other intermines
Show the histone modifications targeted by a particular project.
For a particular project show the histone modifications and developmental stages targeted.
Show all features and their chromosome location for a particular project. NOTE: CHROMOSOME LOCATIONS TEMPORARILY UNAVAILABLE - BACK SOON.
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).
All submissions with a given protocol type
All the protocols submitted
All RNAi reagents used in the modENCODE project
All the submission with results of a certain type
All the submissions using a given strain
All Strains used in the modENCODE project
For a particular submission or list of submissions show all the binding sites identified and their chromosomal locations.
Show all Origins of replication identified by a particular submission.
Show all the located features for a given submission
Show all the reagents for a given submission.
For a particular submission or list of submissions 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).
For a particular list of submissions show the binding sites found within a specified chromosome location at a specified developmental stage.
For a particular submission or list of submissions show all the binding sites identified within a certain chromosome location.
For a particular submission or list of submissions show all the binding sites at a specified developmental stage.
For two submissions or lists of submissions show overlapping binding sites. Note: overlapping does not mean a 100% overlap, the overlap can be complete or partial at either end.
All the submission for a certain project, from the most recent one.
Show all the binding sites within a specified chromosome location at a particular developmental stage for a specified gene or list of genes.
Show all the binding sites within a particular chromosome location for a specified gene or list of genes.
Show all the binding sites at a particular developmental stage for a specified gene or list of genes.
Show regions of copy number variation identified for a particular tissue on a particular chromosome.
Show all transcript regions identified in a particular tissue on a specified chromosome.
Show regions of copy number variation identified for a particular tissue within a particular chromosome location.
Show transcript regions identified in a particular tissue at a specified chromosome location and the genes which overlap the transcript.
Show regions of copy number variation identified in a particular tissue.
All antibodies in the modENCODE project
All antibodies used in the modENCODE project
trying to emulate the report produced at berkley
