Release 12.0 of FlyMine adds genome annotation for the ten additionalÂ Drosophila species included in FlyBase release FB2008_02. Homology data between the 12Â Drosophila species from the 12 Genomes Consortium (2007) paper. Data from BDGPÂ in situ and genetic interactions from BioGRID are also added. We have also added more widgets for analysing lists of genes and improved the style and layout of the list analysis page.
Many existing data sources have been updated to the latest versions, new data sources are detailed below. For a complete list of all data included in FlyMine see the ‘Data’ tab above.
- NEW -Â Drosophila 12 genomes. We have added genome annotation for the additional ten sequencedÂ Drosophila genomes from FlyBase release FB2008_02.
- NEW -Â Drosophila 12 genomes homology – homology between 12Â Drosophila genomes, data from the 12 Genomes Consortium (2007). PubMed 17994087
- NEW – BDGP in situ expression patterns.
- NEW – Genetic Interaction data forÂ D. melanogaster, C. elegans andÂ S. cerevisiae from BioGRID.
- NEW – Probe sets from the Affymetrix GeneChip Drosophila Genome 1.0 Array.
- FIX – Some InParanoid cluster names have been fixed.
- FIX – ProteinDomain name and shortName were both showing the short name, now fixed.
- FIX -Â Drosophila UTRs and CDSs now have FlyBase as evidence.
- FIX – Evidence for REDfly TFBindingSites now fixed.
The layout of list analysis pages has been improved. New ‘List Info’ and ‘Link Outs’ sections are added to the top ot the page. Widgets have had a style update, more can be displayed on the screen at once and a menu allows you to open/close them. Loading times of the list analysis page has been greatly improved. Details of new widgets are given below.
- NEW – Orthologues widget – for a list of genes shows counts of orthologues in other organisms using data from InParanoid and homology between the 12Â Drosophila genomes.
- NEW – BDGP in situ expression patterns widget. For a list of genes display the counts expressed or not expressed at the stage ranges tested.
- NEW – BDGP in situ term enrichment. For a list of genes see if any ImaGO terms assigned by BDGP are statistically enriched.
- NEW – Genetic Interactions widget. For a list of genes show genes that genetically interact and the count of genes from the list that they interact with. Data from BioGRID.
- NEW – For a list ofÂ Drosophila genes export all directly to FlyBase’s HitList page.
- NEW – Data from enrichment widgets can now be exported as tab or comma separated files.
- FIX – no longer get an exception after adding elements to an existing list then clicking ‘view all results’ on list analysis page.
- FIX – Column summary buttons and option to save a list now appear on all results tables.
- FIX – Exporting results has been made much faster.
- FIX – GFF3 export now only exports unique rows.
- FIX – Bug with exporting results in IE6 fixed.
- FIX – List upload now ignores duplicate identifiers even if the case doesn’t match.
- FIX – Links to KEGG pathways on the KEGG web site have been corrected.
- FIX – Improved error messages when importing invalid query XML.
- FIX – Constraining a field in the QueryBuilder to ‘has no value’ sometimes didn’t work, now fixed.
Release 11.0 of FlyMine includes an update of data from FlyBase, expression data related to Tiffin motifs has been added and many other data sources are updated. We have also added new widgets and improved menus on results and list analysis pages.
TheÂ D. melanogaster genome has been updated to release 5.5 from FlyBase. Many other data sources have been updated to recent versions, see the Data tab for more details.
- FIX – We now follow part-of relationships when computing transitive closure on the the Gene Ontology. This means that queries that include parents/children of terms now follow part-of relationships as do the GO enrichment widgets.
- FIX -Â D. melanogaster UTRs and CDSs are now retrieved correctly from FlyBase
- FIX – Some minor changes have been made to the ProteinInteraction class – unused attributes have been removed, interacting regions is now filled in.
- UPDATE – InterPro domains for each protein are now retrieved from UniProt with details of the domains taken from InterPro. We now include domains for more organisms.
- UPDATE – As of October 2007, theÂ Drosophila DNAse I footprint (FlyReg) database has fully merged with the REDfly database. The FlyReg website will no longer be updated. Therefore, FlyMine now loads the FlyReg transcription factor binding sites directly from the REDfly database.
- UPDATE – All REDfly identifiers have been updated.
- UPDATE -Â C. elegans RNAi phenotype data from WormBase have been remodeled. Every phenotype now has a flag for ‘Observed’: true/false. Some phenotypes show a penetrance range.
- NEW – Five moreÂ D. melanogaster RNAi screens added from the DRSC.
- NEW – A subset of Tiffin motifs are now correlated with known expression patterns.
We have changed the way we present orthologue data fromÂ InParanoid to make it simpler and more obvious. Orthologues and Paralogues now appear in a single Homologue class which has a type of ‘orthologue’ or ‘inParalogue’, we no longer use the terms ‘main’ and ‘secondary’. Please contact us if you have any problems with this.
When viewing a list of genes on a list analysis page there is now an orthologue conversion section in the top right. Select an organism to view a results page of orthologues in that organism to export or create a new list.
New widgets have been added to protein and genome feature list analysis pages. Enrichment widgets now include the option to choose Benjamini-Hochberg or Bonferroni error correction. Benjamini-Hochberg is the default and is less stringent. Enrichment and table widgets can now be opened in a new window and have the option to select multiple categories (e.g. multiple GO terms) and display/export all data from those categories.
- NEW – A chromosome distribution widget is now shown on list analysis pages for any located genome feature (e.g. genes, exons, binding sites).
- NEW – Enrichment widgets added to protein list analysis page:
- InterPro protein domains.
- GO terms (queried via corresponding genes).
- UniProt protein features.
- UniProt keywords.
- NEW – Enrichment widget results can be filtered on maximum p-value.
- FIX – clicking on bars of chromosome distribution widget now gives correct results with multi-organism lists.
- FIX – links on GO enrichment now give results forÂ A. gambiae andÂ A. mellifera
- NEW – ‘Add all’/’Remove all’ links added to each issue section on list upload page – making large lists easier to manage.
- NEW – Issues on the confirmation page now have links to open report pages in a new window.
- FIX – Confirmation page no longer resets if an invalid list name is entered.
- FIX – List name is no longer pre-filled with the last entered list name.
Other user interface changes
- NEW – Template query forms include an ‘XML’ link to export an XML representation of the query.
- NEW – Export, Create List and Add To List are now in a menu bar above results tables, combined with previous/next navigation.
- NEW – Open/closed state of sections on report and list analysis sections is now ‘sticky’ for your current session.
- FIX – Improvements to error checking and messages when importing XML queries/templates.
- FIX – Selections don’t reset if an invalid name entered when performing list combination operations.
- FIX – Improved error handling on results page when selecting objects to save and list name.
Release 10.0 of FlyMine includes an update of data from FlyBase, a newÂ A. gambiae gene expression data set and some user interface changes.
TheÂ D. melanogaster genome has been updated to release 5.4 from FlyBase. We have added a new microarray-based gene expression data set for the life cycle ofÂ A. gambiae. ‘Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster.’ (Koutsos et al 2007 -Â PubMed).
Other data changes:
- FIX – duplicate introns have been removed forÂ D. melanogaster andÂ D. pseudoobscura, FlyMine used to infer introns but they are now imported from FlyBase.
- FIX – introns are now created on the correct strand forÂ A. gambiae andÂ A. mellifera.
- FIX – orthologues forÂ A. gambiae,Â A. mellifera andÂ A. aegypti now reference genes as well as translations, they will now appear in results of more template queries.
- FIX -Â D. pseudoobscura ‘Unknown’ assembly groups are no longer created as chromosomes.
- FIX – the ‘localised’ category has been removed for fly-FISH expression data, the data now just shows whether a gene is expressed or not at a particular stage.
The List analysis page has a new ‘Convert’ section for instant conversion between common types (genes, proteins, transcripts and exons). Counts of each type are displayed for a list – e.g. the numbers of proteins, transcripts and exons found for a list of genes. Clicking on the type will bring up a results table from which you can export identifiers, sequence or create a new list.
We have added links to more external databases from report pages – e.g. to model organism databases and REDfly. We now have a simple configuration system for links so if you have suggestions of other databases it would by useful to link to please let us know – support[at]flymine.org.
Tutorial and FAQ
User interface changes
- NEW – the queries run when clicking on graphs or tables in list analysis widgets now include more information.
- NEW – number of rows shown in results tables is remembered.
- FIX – performance improvement for uploading lists with more than 1000 elements.
- FIX – fixed problem where user was logged out or history was lost when returning to the home page.
- FIX – uploading a list from a file is fixed on Safari.
- FIX – it is now more obvious when long text entries have been truncated in results tables.
- FIX – fixed ‘div has no properties’ error in templates tab if user created two templates with the same title.
In release 9.0 we have updated theÂ D. melanogaster genome to release 5.3 and theÂ A. gambiae genome to release AgamP3.4. We have added mRNA localisation data from Fly-FISH (Krause lab) and updated many other sources of data.
TheÂ D. melanogaster genome has been updated to release 5.3 from FlyBase. TheÂ A. gambiae genome has been updated to release AgamP3.4 from Ensembl. Note that with this genome build the identifier scheme has changed – the primary identifiers forÂ A. gambiaefeatures now used in FlyMine are those from VectorBase.
mRNA subcellular localisation data forÂ D. melanogaster from Fly-FISH has been added. There is a new widget on the gene list analysis page to display the numbers of genes in the list that are localised, not localised or not expressed.
Other data changes
Many data sources have been updated to the latest available versions. See the Data tab for more details.
- NEW – Four moreÂ D. melanogaster RNAi screens added from the DRSC.
- UPDATE – All 14 screens from the DRSC have a standardized results annotation, making it easier to query all of them simultaneously.
- FIX – first authors of publications are now set correctly.
- FIX -Â D. melanogaster Affymetrix probes no longer have genome locations – the locations were previously for an old genome assembly.
- FIX -Â A. mellifera genes and proteins are now linked together where possible, GO annotation is now attached to genes.
- FIX – evidence for proteins from UniProt is correctly set to Swiss-Prot or TrEmbl.
User interface changes
- NEW – spaces can be used as separators again in the list upload page – gene names with spaces should be quoted – e.g. “even skipped”.
- NEW – widgets and template sections are now collapsed in list analysis page to improve page navigation.
- FIX – list upload from a file now works on Safari.
- FIX – FASTA export for Translation sequence is now fixed.
- FIX – links to VectorBase now correctly access gene pages.
- FIX – annoying ‘Found 1 match(es) message removed from results page.
- FIX – correct template name/description displayed when clicking on ‘Show in table’ in a report page.
- FIX – some classes weren’t listed in the class chooser in the QueryBuilder tab, now fixed.
- FIX – text in template form dropdowns should now always be displayed correctly.
- FIX – fixed bug with setting ascending/descending sort order in QueryBuilder.
In release 8.2 we have added new ways to link to FlyMine, optional organism constraints to many templates and changed the publication widget on the list analysis page to show statistical enrichment.
Link to FlyMine
In response to requests from other sites you can now link directly to FlyMine list analysis pages with any list of identifiers. List analysis pages show graphs, tables and statistical enrichment for properties of a list – e.g. gene expression, protein domains, publications and pathways. You can also link into FlyMine with, for example, a protein identifier and request to see the corresponding gene report page. SeeÂ this document to find out how to create links.
The publication widget on the gene list analysis page now shows statistical enrichment of related publications. This is a great way to find the most relevant publications for a given gene list and may help you interpret the list. Gene/publication relationships are loaded fromPubMed.
Optional organism constraints
Many templates now have an optional constraint on organism to make it easier to use these templates with gene symbols.
- FIX – template form layouts have been improved.
- FIX – totals are now displayed correctly in the FlyAtlas widget on list analysis pages.
- FIX – wildcards now work in quick search again (e.g. you can search for ‘zen*’).
- FIX – Lists/Templates pages are now correctly reset if text is removed from filter box.
- FIX – logging out on some pages gave an error message, this is fixed.