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
We have added a tutorial on creating and using lists in FlyMine, see theÂ help page. There is also a list ofÂ Frequently Asked Questionslinked to from the header.
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.
FlyMine is running a joint workshop with FlyBase in Cambridge (free of charge). For more information and to sign up seeÂ here
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.
In release 8.1 of FlyMine we have made some major changes to the layout of FlyMine. This has been done in response to feedback from users and to make the most exciting parts of FlyMine more obvious. We have also added public lists and a new help system.
A newÂ header provides tabs for easy access to the major areas of the site. TheÂ Templates andÂ Lists tabs link to new search pages that show all templates/lists and update as you type keyword search terms. You can also restrict by data category and, if you are logged in, restrict to your favourites or own saved data. TheÂ search bar in the header is a quick way to search identifiers and now also templates and lists.
The updatedÂ home page layout introduces the main concepts – Data categories, Templates, Lists and the QueryBuilder. There is also space for us to highlight new or interesting templates and public lists.
In response to user feedback we have renamed some elements of the FlyMine interface to make them more obvious.Â ‘Bags’ are now calledÂ ‘Lists’,Â ‘Aspects’ are nowÂ ‘Data categories’. We also refer now refer toÂ Report pages instead of the computer speak:Â Object details pages and aÂ List analysis page instead of aÂ Bag details page. Hopefully it won’t cause confusion for too long.
Another major development is the introduction ofÂ public lists. These are lists that we create and make available for everyone to use, typically they will be derived from a publication. In this release we have added public lists based onÂ FlyAtlas expression in the adult fly tissues andÂ FlyTF transcription factor lists. Click on an example on the home page to see a list analysis page with graphs, tables, statistical enrichment and the results of templates run for the list. We can add new public lists at any time, please contact us if you have a suggestion.
List Analysis Widgets
We have added two newÂ ‘widgets’ to the analysis page for a list of genes. These show statistical enrichment of InterPro protein domains within a list of genes and the publications that reference the most genes from the list (data from PubMed). We will continue to add to the list analysis page in every release, so let us know if you have any suggestions.
A new context sensitive help system has replaced the FlyMine manual. On every page there is a ‘?’ icon to the top right, click this to get help with the current page and find out what you could do next. The help should now be briefer and more readable.
- Results page
- FIX – column summaries sometimes gave misleading results when counting unique rows.
- FIX – the total number of rows and unique rows in summaries now update correctly in Safari.
- FIX – colons are now allowed in list/template names.
- FIX – occasional issues with creation dates of templates/lists are fixed.
- Report page
- NEW – the bottom of each report page shows any lists (public or saved) that contain the object.
- NEW – template descriptions are now included when inline tables are open.
- FIX – some issues with the view list and sort order on Internet Explorer are fixed.
- FIX – when using LOOKUP constraints can now convert wildcards that match an incorrect type – e.g. convert EVE_DROME* (a protein identifier) to a gene.
- FIX – LOOKUP constraints and list upload now accept names that contain spaces – e.g. ‘even skipped’ for the eve gene.
- FIX – sort order is now remembered for saved queries, doesn’t get reset when removing elements from view list.
In release 8.0 we have updated the data model for protein interactions, protein structure and orthologues to make them easier and faster to query. We also include three new data sets: Tiffin (predicted regulatory motifs), anoEST (A. gambiae EST clusters) and predicted 3-D protein structures for A. gambiae domains. A new type of constraint is used in template queries which now allows you to enter any identifier or symbol.
- NEW – D. melanogaster predicted regulatory motifs and functional sites (motif instances) from theÂ Tiffin database. Note these have been mapped to the release 5.0 genome sequence.
- NEW – A. gambiae EST and EST clusters from theÂ Imperial College London Centre for Bioinformatics.
- NEW – A. gambiae protein domain 3-D structure predictions fromÂ Kenji Mizuguchi. This data provides structure predictions for regions of A. gambiae proteins that correspond to a Pfam domain.
- NEW – H. sapiens and M. musculus protein information included from UniProt, we already include InParanoid orthologues to these organisms.
- User Interface
- NEW – LOOKUP constraints. Most template queries are now updated to use a new type of constraint. Now you don’t need to enter a specific type of identifier – for example for the D. melanogaster gene zen you could enter ‘zen’, ‘CG1046’, ‘FBgn0004053’ or ‘zerknullt’ and get the same result. You could even enter a protein and or transcript identifier and it would find the gene.
We are running a half day workshop on using FlyMine in Cambridge UK on June 20th. This is part of a joint workshop with FlyBase, half a day will be devoted to each. The workshop is free of charge, for more information and to sign up seeÂ here.