A Database of Drosophila Genes & Genomes

FB2009_08, released September 11, 2009
 

News and Announcements

FlyBase News
hide Gene Ontology section changes ... Jul 2009

FlyBase uses Gene Ontology (GO) terms to describe the function, biological role and subcellular location of gene products. This release sees a number of improvements to the Gene Ontology section of the gene report pages.

The major change, in response to user feedback, is that all GO terms supported by experimental evidence1 in primary research papers are now grouped in a separate section. This will allow users to distinguish more readily characteristics that have been experimentally verified in Drosophila from those that are predicted based on similarity to other gene products or asserted in papers without the supporting experimental data being shown. The new sections are labelled 'Terms Based on Experimental Evidence' and 'Terms Based on Predictions or Assertions' - we indicate how many terms appear in each (note that the same term may appear in both sections).

Capturing all data from the vast Drosophila literature is a slow process and we do not yet have GO terms assigned for all genes. We have become aware that there is some confusion in distinguishing gene products that are truly uncharacterised from those that have no terms because they have not yet been thoroughly examined by a curator. To address this, for gene products where we can't find any evidence for GO terms for one or more aspect of GO, we have added a new section at the top of the gene ontology section with an explicit statement to that effect 2. We also include a date to indicate when a curator last reviewed all information for the gene product.

GO terms for Drosophila gene products are often predicted based on homology to other sequences, the presence of a well-characterised protein domain or inferred from other assigned GO terms (e.g. if a gene product has transcription factor activity we could infer it is found in the nucleus). To make it easier to see the basis of such term assignments, we have added links to the relevant sequences, domains and GO terms. Where possible we also indicate the species of the homologous gene products.

Finally, not all GO terms are assigned to Drosophila gene products by FlyBase. We now acknowledge the source of external contributions, most notably from UniProtKB, in the evidence column of the GO section.

If you have any suggestions or comments regarding the GO terms assigned to your favorite genes or how this information is presented please contact FlyBase.

(1) Note: Experimental evidence comprises of terms assigned with the evidence codes: 'inferred from direct assay', inferred from genetic interaction', 'inferred from mutant phenotype' and (the infrequently used) 'inferred from expression pattern'.

(2) Note: In the precomputed gene_association.fb file these 'known unknowns' will continue to be annotated with the most general (root) GO terms 'molecular function', 'biological process', or 'cellular component' as appropriate using the 'no data available' evidence code.

hide Mapped Features Reorganized ... Mar 2009

The "Mapped Features & Mutations" section of the gene report pages, which is found under the "Gene Model & Products" heading, has been renamed and reorganized in the FB2009_03 release. This section is now called "Mapped Features" and contains only information on wild-type features associated with the gene, such as regulatory regions and regulatory protein binding sites. The data on characterized mutations and other sequence variants (including rescue fragments) have been moved to the "Mutations Mapped to the Genome" section of the report for the allele associated with the molecular lesion; the sequence coordinates of aberration breakpoints have been moved to the relevant aberration report; and sequence location data for transgenic insertions are now presented in the insertion report. All mapped features may be viewed in GBrowse by toggling the "Select All" option for "Mapped features"; precise coordinates and comments are included in the GBrowse html table option.

hide The FB2009_01 release ... Jan 2009

The FB2009_01 release includes an overview of the precomputed files generated by FlyBase, and several new ways to view molecularly localized aberrations, including by entire arm or chromosome.

In GBrowse a new view is available that shows molecularly localized genes and aberrations. To select this view choose "Drosophila aberrations" from the "Data Source" menu in the main GBrowse window. It allows you to view aberrations up to 3Mb in size, and will also display the location of transposon insertion sites when you look at an interval of less than 300Kb.

aberrations

Aberrations that delete the entire interval displayed are referred to as "Spanning Aberrations" and hovering over the dark red line produces a table listing these aberrations. Hyperlinks within the table allow you to navigate to the report on each aberration.

spanning_aberrations

When you place your mouse over an aberration an alphabetical list of all the genes predicted to be affected by the aberration (deleted or truncated) appears. Clicking on the aberration will take you to the FlyBase report page for the aberration. Similarly, hovering over a gene or transposon insertion site displays information about it, and clicking on it takes you to the corresponding report.

genes_in_an_aberration

Aberration Maps for Arms and Chromosomes

Images showing all molecularly localized aberrations and genes by arm or chromosome are also availabe from the Aberration Maps page listed in the Tools menu. The links on the page take you to the left end of the arm or chromosome, and the entire extent can be viewed by scrolling to the right. Like the new GBrowse view, information about an aberration or gene can be obtained by hovering over it. A copy of the images of the arms and chromosomes can be downloaded from the aberrations section of the precomputed files page.

Deficiency Maps in Aberration Reports

Each FlyBase report describing one of the Df()ED, Df()Exel, Df()BSC and Df()FDD class of aberrations contains an image showing the genes predicted to be uncovered by the aberration, and overlapping or neighbouring molecularly localized aberrations. Clicking on a gene or aberration will take you to the appropriate report. You can also move to the new GBrowse view of the molecularly localized aberrations by clicking on the "GBrowse" link listed on the left hand side of the picture.

hide Changed E-mail for Help ... Oct 2008

FlyBase has eliminated the e-mail address flybase-helplinkmorgan.harvard.edu because that address had been hopelessly compromised by spammers. Although the address had been hidden behind our help form in recent years, it was exposed on the site for many years prior and had become the source of a vast and relentlessly growing quantity of spam. If you use the Contact FlyBase help form on the web site you will not be affected by this change. If you prefer to e-mail us directly you will need to use the help form to ask for the new address. This address may change periodically in the future, but you will always be able to reach us via the Contact FlyBase form and we will continue to provide the direct e-mail address to those who request it.

hide Chromosome Maps ... Sep 2008

We are introducing chromosome maps for the 12 sequenced Drosophila species with the FB2008_08 release, which are based on the ones publised in Schaeffer et. al., Genetics 179: 1601-1655 2008, and the well characterised physical and genetic maps for Drosophila melanogaster. The maps show the sequence scaffolds aligned to the polytene chromosome maps for the Muller elements of each species. For more information on the syntenic relationships among the 12 sequenced genomes, their standard chromosomal numbering and corresponding Muller element please see the Muller Element Arm Synteny Table. The different Muller elements of the species selected can be viewed by using the controls at the top right hand side of the map.

The aligned sequence scaffolds are indicated on the maps in blue and and moving your cursor over a scaffold will produce a yellow box that corresponds to a window in GBrowse.

chromosome map example

The location of the GBrowse window is updated as you move along a sequence scaffold and clicking on the yellow box will take you to the corresponding location in GBrowse. The controls at the top of the page allow you to alter the size of the GBrowse window.

You can move around the chromosome maps by using the arrows at the top left hand corner of the map, or by dragging on the surface of the map. Alternatively, you can change your location by dragging the blue box shown in the overview map at the bottom right hand corner of the map window. The "Center" button allows you to rapidly return to the initial view of the map. You can also zoom in or out of the maps by clicking on the "+" and "-" buttons found under the arrow keys in the top left hand corner of the map in a similar fashion to Google Maps.

We hope you find the maps useful and welcome your comments and suggestions.

FlyBase Announcements
hide Apollo Support ... Sep 2006

From this point forward FlyBase will be providing Apollo viewable annotation data in chado-xml format only. The latest version of Apollo has been modified to retrieve annotation data via the web in this format. Therefore, we recommend that you upgrade to the latest available version of Apollo

We will no longer provide annotation data in GAME-XML format and while Apollo is still able to load and view existing GAME-XML data the data files must be available on the local machine as web retrieval of GAME files is no longer supported.

Please be aware that when Apollo is retrieving annotation data from the web it is obtaining precomputed chunks of xml. While the pieces have been generated to not span any gene models retrieval by sequence range may not result in the exact sequence requested being loaded into Apollo.

Please use the contact FlyBase form to send questions and requests for help to FlyBase.

hide Linkouts in FlyBase ... Mar 2006

FlyBase offers direct "linkouts" from our gene report pages to other web-based Drosophila data services. . The FlyBase Consortium wishes to thank the organizers and developers of these data sets for helping us provide a great deal of valuable information on Drosophila genes and genomes.

  • BDGP in situ Gene Expression Database (http://toy.lbl.gov:8888/cgi-bin/ex/insitu.pl)
  • Drosophila melanogaster Exon Database (http://proline.bic.nus.edu.sg/dedb/index.html)
  • Drosophila RNAi Screening Center (http://www.flyrnai.org/)
  • FLIGHT - Integrating Genomic and High-Throughput data (http://flight.licr.org/)
  • Fly GRID Interaction Data (http://biodata.mshri.on.ca:80/fly_grid/servlet/SearchPage)
  • FlyMine - integrated genomics and proteomics (http://www.flymine.org/)
  • NCBI Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/projects/geo/)
  • Heidelberg Database for RNAi Phenotypes (http://www.dkfz-heidelberg.de/signaling/ernai/ernai.html)
  • Hybrigenics Drosophila PIMRider (http://pim.hybrigenics.com/pimriderext/droso/index.html)
  • Yale Developmental Gene Expression (http://genome.med.yale.edu/Lifecycle/)
  • InParanoid computed orthology calls (http://inparanoid.cgb.ki.se/index.html)
  • PANTHER ClassificationSystem (http://www.pantherdb.org/)

In addition to these links FlyBase also provide direct links to the Drosophila records in the major international nucleotide, protein and bibliographic databases.

Community News & Announcements
hide Reactome Pathway Database User Survey ... Sep 2009

Reactome is committed to providing access to high-quality pathway information and helpful data analysis tools.  With this in mind, we are actively soliciting comments from the fly research community in order to assess community needs.  We are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome site and tools.

You can access the survey at: http://tinyurl.com/l48zzq.

hide DPGP announcement ... Sep 2009

DPGP announces the availability of Release 1.0 of "50 D. melanogaster genomes"

The Drosophila Population Genome Project released today the reference version (Release 1.0) of the initial sample of Drosophila melanogaster genomes sequenced by the DPGP using first generation (single-end and 36 bp) Solexa/Illumina technology and assembled using maq 0.6.8.

The sample consists of the sequences for the 5 major chromosome arms (X, 2L, 2R, 3L and 3R) for 37 inbred genomes from Trudy Mackay's set of inbred lines sampled in Raleigh, NC and a set of sequenced chromosomes (7 chrXs, 6 chr2s and 5 chr3s) from a sample of Malawi isofemale lines that were inbred using balancers. The data for each chromosome arm are in FASTQ format and list of the regions of residual heterozygosity and identity by descent are attached. Repeated sequence are filtered (set to "N"). The "raw data" are available in the NCBI Short Read Trace Archive.  The average coverage of the unique portions of all these genomes is >10X.

Release 1.0 data can be accessed at http://www.dpgp.org.

hide Sharing prepublication data ... Sep 2009

Please see the forum on sharing prepublication large-scale data at Nature.

hide Szeged Closure ... Jun 2009

Szeged Drosophila Stock Centre will terminate its activity by June 30, 2009. Some of the collections will be transfered to other centers, while others will not be available in the future.

For more information please contact Peter Maroy, University of Szeged.

hide P[acman] BAC libraries ... Apr 2009

Dear Drosophilist,

At the recent fly meeting in Chicago, we reported on two BAC libraries (a 20 kb and an 80 kb library) cloned in the P[acman] recombineering and transgenesis vector system. This new resource makes recombineering and transgenesis easier, and we believe that it will be a useful addition to the Drosophila toolkit. A manuscript describing the libraries and applications is now in press at Nature Methods and should appear online in May: "Versatile P(acman) BAC Libraries for Transgenesis Studies in Drosophila melanogaster" by Koen J. T. Venken, Joseph W. Carlson, Karen L. Schulze, Hongling Pan, Yuchun He, Rebecca Spokony, Kenneth H. Wan, Maxim Koriabine, Pieter J. de Jong, Kevin P. White, Hugo J. Bellen* and Roger A. Hoskins.

To learn more about the project, go to our home page at http://www.pacmanfly.org. In addition to information on P[acman] reagents and protocols, you will find a link to a genome browser for identifying P[acman] clones containing genes and genomic regions of interest. Provide the CG number or gene symbol for your gene (wildcard * allowed), and you will find genomic clones from the two libraries that encompass the gene. Additional search options are described on the browser page. If clone coverage is limited in your region of interest, then toggle on the partially mapped clones, which are anchored to the genome by alignment of one end sequence only, for more choices. Clicking on a clone in the browser will take you to a page with the deduced sequence of the genomic insert and a link to the BACPAC Resources website, where clones can be purchased on a cost-recovery basis.

* Questions about this resource should be directed to Hugo Bellen (hbellenlinkbcm.tmc.edu).

Best,

Roger Hoskins
Koen Venken
Hugo Bellen

hide Consultation on the 2009 White Paper ... Jan 2009

Dear Fly Person,

Every two years the Drosophila Board, together with extensive input from the fly community, revises and publishes the Drosophila Board White Paper. This document is extremely useful for informing NIH and NSF of our top research priorities. Past White Papers have helped to justify funding for valuable community resources such as insertion mutations, cDNA collections, FlyBase and fly and molecular stock centers. The White Paper is scheduled for an update this year, and I am writing to ask for your input.

Please download and read the latest version of the White Paper:

http://flybase.org/static_pages/news/whitepapers/DrosBoardWP2007.pdf

  • Which projects on the list remain high priority?
  • What are the bottlenecks to current research using Drosophila?
  • What do you see as the emerging projects or technologies that should be encouraged or supported?

Your input to this process is essential for maintaining and expanding our research tools. Please take the time to send your comments and ideas so that our stated priorities accurately represent the fly community for the next few years. Respond to me, to your regional Representative on the Board, or to any member of the Board. Our email addresses can be found at:

http://flybase.org/static_pages/news/board.html

Thank you for your help,

Carl Thummel
President, Drosophila Board

hide ENCODE-modENCODE Consortia Data Release Policy ... Nov 2008

NHGRI announced the Data Release Policy agreed for the ENCODE and modENCODE Projects.

hide modENCODE White Paper ... Oct 2008

The modENCODE White Paper [PDF] proposes

  • "The sequencing of 8 additional fruitfly and 7 nematode species selected specifically for their potential to enhance modENCODE's goal of complete functional annotation of DNA elements in the genomes of Drosophila melanogaster and Caenorhabditis elegans."
hide Draft ENCODE Data Release Policy ... Sep 2008

The NHGRI would like input from the fly community on the draft Data Release Policy that has been developed for the ENCODE and modENCODE Projects.

NHGRI has updated the data release plan for the ENCODE (Encyclopedia of DNA elements) and model organism ENCODE (modENCODE) Projects (see http://www.genome.gov/ENCODE and http://www.genome.gov/modENCODE, respectively), which are designed to identify all functional elements in the genomes of human (ENCODE), and Drosophila melanogaster and Caenorhabditis elegans (modENCODE). NHGRI has designated both ENCODE and modENCODE as "community resource projects." Accordingly, the data release plan is based on the principles set forth in the Fort Lauderdale agreement (http://www.genome.gov/Pages/Research/WellcomeReport0303.pdf). This update provides more specificity to the data release guidelines.

The Fort Lauderdale agreement noted that the success and utility of community resource projects is based on mutual and independent responsibilities for the production and use of the resource by the resource producers, the resource users, and the funding agencies. The update of the ENCODE/modENCODE data release plan has been developed in consultation with the members of the ENCODE and modENCODE Consortia, and with the External Consultants Panel for the projects. As the plan is intended to take into account the needs and responsibilities of the resource users, we would like to offer the research community an opportunity to provide feedback on the proposal before the plan is finalized. Comments on the plan should be sent to Encodelinkmail.nih.gov by Wednesday, October 15, 2008.

hide Drosophila Genetic Reference Panel White Paper ... Jun 2008

The Drosophila Genetic Reference Panel White Paper 2008 [PDF] proposes

  • "The sequencing of a D. melanogaster genetic reference panel of 192 wild-type lines from a single natural population which have been inbred to homozygosity, and for which extensive information on complex trait phenotypes has been collected. This will create: (1) A community resource for association mapping of quantitative trait loci. Within this project we will demonstrate such mapping and provide candidate quantitative trait polymorphisms for traits relevant to human health. (2) A community resource of common Drosophila sequence polymorphisms (SNPs and indels) with a minor allele frequency (MAF) of 0.02 or greater. These variants will be valuable for high resolution QTL mapping as well as mapping alleles of major effect, molecular population genetic analyses, and allele specific transcription studies, among others. (3) A 'test bench' for statistical methods used in QTL association and mapping studies for traits affecting human disease."
hide Drosophila Network News (bionet.drosophila)
  • Search and read Drosophila network news at www.bio.net
  • Post a new article to dros/bionet.drosophila via the BIOSCI mail-Usenet gateway: droslinknet.bio.net