News
We have extended the Gene Expression section of each gene page to support the display of quantitative expression data, and are now showing data from two publications:
- Marguerat S, Schmidt A, Codlin S, Chen W, Aebersold R, BählerJ. 2012. "Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells." Cell 151:671-683.
- Wu JQ, Pollard TD. 2005. "Counting cytokinesis proteins globally and locally in fission yeast." Science 310:310-314.
We will also soon refine the display of the new expression data, and can add more datasets upon request. We thank Sam Marguerat for preparing the data from both papers for inclusion in PomBase.
We have also updated the PomBase site to include manual curation through April 4, 2013, and we have updated the "all gene names" file on the PomBase ftp site. The new file is available at
ftp://ftp.ebi.ac.uk/pub/databases/pombase/pombe/Mappings/allNames.tsv
Carl Singer, who was an integral part of the yeast research community for many years, passed away on February 8, 2013. Throughout his career, Carl supported yeast research both with his engineering expertise and with his good cheer. In tribute to Carl, the Singer family has now set up The Carl Singer Foundation, a charitable foundation dedicated to supporting scientific education in the field of yeast genetics. Questions about the foundation may be directed to Harry Singer at harry [at] thecarlsingerfoundation.org.
Carl’s family would be happy to receive memories of Carl’s life at regards [at] singerinstruments.com.
H/T SGD
Dear Pombe Fans, Please remember the imminent deadline (Monday 8th April) to register and submit abstracts for Pombe 2013: http://events.embo.org/13-pombe Abstracts are also required from all who have already been invited to talk. And do book your accommodation if you haven't yet done so. More details are in previous email forwarded below. Cheers, -Jürg & Jacky From: On Behalf Of Bahler, Jurg Sent: 18 March 2013 17:49 To: pombelist at sanger.ac.uk Subject: [Pombelist] Pombe 2013: Accommodation, registration & abstracts Dear Pombe Afficionados, Only three weeks left to register and submit abstracts for Pombe 2013, by Monday 8th April: http://events.embo.org/13-pombe Speakers for 10 plenary talks and all workshop talks will be selected from abstracts, and there will be attractive poster prizes. Payment is only requested after registration, by 10th May. Important: if you require accommodation, please do book this real soon now. Especially the most cost-effective student accommodation (comfortable, with private bathrooms) may not be available much longer, as it will be put on general sale shortly. Both hotels and student accommodation will sell out in June, so you have to arrange it now. Information on accommodation is available here: http://events.embo.org/13-pombe/application.html We will provide a number of free registrations for which you can apply during online registration (a few of which are reserved for student members of The Genetics Society: you become eligible if you join them now). The meeting is also supported by the Biochemical Society, so if you are, or become, a member you can apply to them for student bursaries or, if you have been a member for at least 1 year, also for travel grants. We highly appreciate all the generous contributions from our sponsors so far: Platinum: EMBO Gold: Biochemical Society, Genetics Society, Formedium, Sunrise Science Products, Singer Instruments, F1000Research, PomBase/Wellcome Trust Silver: MDPI - Open Access Publishing, Hybrigenics, Infors, Life Technologies, Bioneer Bronze: Nature Communications, m2p labs, Imsol, Open Biology We look very much forward to welcoming you in London this June! All the best, -Jürg & Jacky
We have once again updated the data available on the PomBase web site. The data now includes manual curation through March 6, 2013.
We now expect to be able to update PomBase data every month, and will soon have an automated pipeline in place. We thank all of you for your patience during the long months when updates were infrequent.
You should also see a few small improvements in the site:
- Ontology term pages now display the text definition for each term.
- FASTA sequence retrieval should be quicker, and less likely to time out, for large gene lists.
- There has been some tidying of the display of "extension" data for GO and phenotype annotations.
Last month we noted an intermittent problem with the "Reference" column display in the data tables. The occurrence of this problem should now be greatly reduced, so please let us know if you see it recurring.
As usual, please don't hesitate to alert us of any other problems with data or site performance, or if you have any questions.
We have updated the data available on the PomBase web site. The data now includes manual curation through December 17, 2012, and reflects complete curation of an additional 70 papers.
We have also made some improvements "under the hood" that should make gene page loading much faster. Please let us know if you have any problems with gene pages loading slowly or incompletely, whether or not you have reported issues in the past.
We are aware that there is an intermittent problem with the "Reference" column display in the data tables -- sometimes a PubMed ID appears instead of an author name and year. This problem will be fixed as soon as possible. Please alert us if you notice anything else odd or wrong.
We are pleased to announce that we have updated both data and web site features for PomBase.
Most importantly, we have added new data types, and upgraded the gene pages to display them.
We have also added more annotations of existing data types, bringing the web site content up to September 11, 2012. The new annotations include the first contributions to come in via the new community curation system, and we thank the researchers who are participating in the initial phase of community curation.
New annotation types:
- Phenotype annotations now use the Fission Yeast Phenotype Ontology (FYPO), and include allele details, expression levels, and experimental conditions. With FYPO, more detailed phenotypes can be described, and links between terms for related phenotypes support improved phenotype searches.
- Many GO annotations now include "annotation extensions" that provide additional specificity. For example, extensions may capture the substrate of a catalytic activity, the cell cycle phase during which a function or process occurs, or any of several other types of supporting information for the annotation. Annotation extensions are described in more detail below.
You can see these new data types on many gene pages, such as cdc2 or pka1.
New web site features:
- Annotation display - Gene page GO and phenotype displays have been revamped to show new annotation types described above.
- Ontology term pages - Each ontology term ID now links to pages with information about the term and lists of genes annotated to it.
- Ontology graph links - GO and phenotype annotation sections now include links to graphical ontology displays in the genome browser.
- Sequence highlighting - Sequence download now offers an option to show colour highlighting of regions such as UTRs, introns and exons.
- Versions - Each gene page now shows the current data version in the format PomBase:x.y, where x is the Ensembl Genomes (EG) version, and y is the Chado version. The sequence, and sequence feature locations, remain stable within any EG version, whereas annotations change with each Chado update.
- Protein family information is now included in the Protein Features gene page section.
- The Protein Feature section includes a link to the Pfam entry for a protein.
- Transcript source data (e.g. for UTR coordinates) is now displayed in the Transcript Features section.
- A Documentation page contains links to relevant portions of the Ensembl Genomes documentation. (More documentation will be added over the coming months.)
What are annotation extensions?
Annotation extensions are a form of supporting data that can be added GO annotations (or other ontology annotations) to capture additional details not provided by the ontology term itself.
The information in GO annotation extensions encompasses several effector-target relationships, such as
- localisation dependencies
- substrates of functions, e.g. targets of a protein kinase -- see the has_substrate extensions on Cdc2's "protein serine/threonine kinase" (GO:0004674) annotations
- activators and inhibitors
- regulation targets of signalling pathways or transcription factors
Additional extensions describe spatial and temporal aspects of processes. For example, several S. pombe annotations now include extensions that indicate in which phase of the cell cycle a gene product is found in a cellular component or involved in a process -- see the pka1 annotations to "nucleus" (GO:0005634) and "cytoplasm" (GO:0005737).
You may also find the GO wiki page on annotation extensions informative, although it is primarily aimed at curators.
Annotation extensions can also be used with phenotype annotations. The most common usage of phenotype annotation extensions is to capture which gene, protein, etc. was used in an assay. For example, the sam5 (G441E) mutation of pka1 causes nuclear accumulation of Ste11. This is represented by annotation to the ontology term "nuclear protein accumulation" (FYPO:0000255), with the extension "assayed_using(PomBase:SPBC32C12.02)". Extensions can also indicate expressivity or penetrance for a phenotype.
We are pleased to announce that the PomBase web site, www.pombase.org, is now fully live; the preview phase has ended. The site has been updated with an assortment of new features, datatypes, and bug fixes.
More recent data, reflecting additions and changes through March 20, 2012, are now available on gene pages and in search results.
The updated site features a Gene List Search that provides behavior equivalent to GeneDB's List Download. You can now type or paste lists into the Gene Systematic IDs and Gene Names filters, and use the Query History to combine a gene list search with other search options. For convenience, there is a direct link to a search page pre-configured to accept a list of systematic IDs available in the Find menu, on the Find page, and here: http://www.pombase.org/spombe/query/builder?filter=12
The Advanced Search also now offers:
- options to search GO, FYPO, and other ontologies by term name or ID;
- autocomplete for ontology term name search;
- ability to search for genes in a region, such as centromeres or telomeres;
- improved organization of filter selections.
We have also fixed a Sequence Download error reported by some users, so that the "CDS", CDS + UTRs", and "CDS + UTRs + Introns" options now retrieve the correct sequences.
In addition, numerous minor improvements have been made. Please send any questions or comments on the PomBase web site to us at <helpdesk@pombase.org>.
A preview of PomBase, the new model organism database for the fission yeast Schizosaccharomyces pombe, has been announced to the S. pombe community for testing and feedback. For more on PomBase, see the NAR Database Issue paper (PubMed abstract) or contact the PomBase staff.
A paper describing PomBase has been published online will be included in the 2012 Database Issue of Nucleic Acids Research. Abstract and open access full text are available.
A paper describing the major findings of the Schizosaccharomyces Comparative Genome Project was published today in Science Express and reported changes are included in GeneDB.
Further details are described in the pombe mailing list posts:
Further information on the pombe mailing list.
Further details are available on the pombe mailing list.
The analysis of the fission yeast deletion collection is now published online in Nature Biotechnology.
Funding was awarded by the Wellcome Trust for a fission yeast Model Organism Database, Pombase.
Fission yeast is one of the 12 key organisms of the reference genomes project. The goal of this project is to completely annotate twelve reference genomes so that those annotations may be used to effectively seed the automatic annotation efforts of other genome.
GeneDB (S. pombe) now uses the latest update to Pfam, release 24.0 and 88.5% of fission yeast proteins now contain a match to at least one Pfam domain (increased from 83% in version 23).
The fission yeast genome and annotation dataset is now available as part of Ensembl Fungi.
GeneDB is now using Version 23 of the Pfam protein family database. A total of 4154 (83%) S. pombe proteins now have at least one Pfam domain or family assignment (compared to 76% for S. cerevisiae), the highest percentage coverage for any eukaryote.
S. pombe GeneDB now includes "deep links" to the Biological General Repository for Interaction Datasets (BioGRID) interaction datasets from the 'Database Cross References' section of the individual Gene Pages.
Dynamic repertoire of the fission yeast transcriptome reveals: 94% of the genome is transcribed; extensive variation in different stages and conditions; global and condition-specific coupling between splicing efficiency and transcription; confirms the majority of introns; refines ~75 gene structures; identifies 453 new transcripts 26 of which were predicted to code for proteins.
The h- mating type region has been provided by Xavier Marsellach and Lorena Aguilar.
Baumann and Zakian labs identify elusive telomerase RNA (PMID:18157152 and PMID:18157149)
Wellcome Trust Advanced Course 'Genome-wide approaches with fission yeast' held in Hinxton.
4th International Fission Yeast Meeting held in Copenhagen.
GeneDB representation of the fission yeast data moved from contigs to chromosomes. See the pombelist archive for details.
The October issue of the journal Yeast is a fission yeast special issue containing 13 articles and reviews commissioned as a result of the European Fission Yeast Meeting, which are FREE to download.
The first fission yeast whole proteome localization study is now published: Matsuyama A. et al (2006): ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe. Nat Biotech 24, 841-7.
The fission yeast database survey is now closed. You can view the survey results here.
The European Fission Yeast Meeting (16th-18th March 2006) and The Fission Yeast Bioinformatics workshop (15th - 16th Mar 2006) both took place at the Wellcome Trust Genome Campus in Hinxton (Cambridge, UK).
Comparative Genomics of Eukaryotic Microorganisms:
Eukaryotic Genome Evolution, Approaches with Yeasts and Fungi
This conference took place from 12th-17th November 2005 in Sant Feliu de Guixols, Spain. Full details can be found here.
Second East Coast Regional pombe Meeting
This meeting took place from November 11-13, 2005 in Miami Beach, Florida.
A project to record published genetic and physical interactions is underway with Mike Tyers and the GRID group at Toronto.
The meeting was held at UC San Diego on August 24-29, 2004.
This issue of Methods includes 11 papers for fission yeast protocols including DNA damage checkpoint assays, cell wall analysis, TAP, nuclear envelope integrity assays, GFP imaging, TS mutant creation and plasmid use and construction. See Methods or click here for details of the papers including PMIDs.
Correlations Between Gene Expression and Gene Conservation in Fission Yeast. Mata J, Bahler J. Genome Res. 2003 Nov 12 PMID:14613978
FELINES: a utility for extracting and examining EST-defined introns and exons. Drabenstot SD et al Nucleic Acids Res. 2003 Nov 15;31(22):e141. PMID:14602934
Genome-wide distribution of DNA replication origins at A+T-rich islands in Schizosaccharomyces pombe. Segurado M, De Luis A, Antequera F. EMBO Rep. 2003 Nov;4(11):1048-53. Epub 2003 Oct 17. PMID:14566325
Retrotransposons and their recognition of pol II promoters: a comprehensive survey... Bowen NJ et al Genome Res. 2003 Sep;13(9):1984-97. PMID:12952871
Egel, R., Copenhagen, Denmark (Ed.) The Molecular Biology of Schizosaccharomyces pombe Genetics, Genomics and Beyond ISBN:3-540-00693-1
Decottignies A, Sanchez-Perez I, Nurse P Genome Res. 2003 Mar;13(3):399-406. PMID:12618370
Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N, Bähler J. Mol Biol Cell. 2003 Jan;14(1):214-29. www.ncbi.nlm.nih.gov/pubmed?term=12529438http://www.ncbi.nlm.nih.gov/pubmed?term=12529438