Release 12.0

Release 12.0 of FlyMine adds genome annotation for the ten additional Drosophila species included in FlyBase release FB2008_02. Homology data between the 12 Drosophila species from the 12 Genomes Consortium (2007) paper. Data from BDGP 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.

Data

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 - Drosophila 12 genomes. We have added genome annotation for the additional ten sequenced Drosophila genomes from FlyBase release FB2008_02.
  • NEW - Drosophila 12 genomes homology – homology between 12 Drosophila genomes, data from the 12 Genomes Consortium (2007). PubMed 17994087
  • NEW – BDGP in situ expression patterns.
  • NEW – Genetic Interaction data for D. melanogaster, C. elegans and 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 - Drosophila UTRs and CDSs now have FlyBase as evidence.
  • FIX – Evidence for REDfly TFBindingSites now fixed.

List Analysis

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 12 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 of 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.

Other fixes

  • 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.
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