3D reconstructed images of the F-actin contractile ring
Issei Mabuchi

Did You Know ... ?

PomBase maintains a number of pages related to fission yeast genome status, with respect to sequencing, publication, etc. Highlights include a set of statistics giving an overview of genome composition and identified genes and other sequence features, and a page summarising the characterisation of known and predicted protein-coding genes.

About PomBase

PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets

News

Friday, 18th Jul, 2014

We have updated the data available on the PomBase web site to include manual curation through July 8, 2014. The gene pages also now display protein modification data from an additional large-scale dataset:

Koch A, Krug K, Pengelley S, Macek B, Hauf S. 2011. Mitotic substrates of the kinase aurora with roles in chromatin regulation identified through quantitative phosphoproteomics of fission yeast. Sci Signal. 4(179): rs6 doi: 10.1126/scisignal.2001588 PMID:21712547

We have also made corrections to some residue positions affected by sequence updates in one of the modification datasets we added last month:

Carpy A, Krug K, Graf S, Koch A, Popic S, Hauf S, Macek B. 2014....

Wednesday, 9th Jul, 2014

We have updated the data available on the PomBase web site. The data now includes manual curation through June 6, 2014. In other improvements, a downloadable file of intron sequence data (FASTA format) is now available, and phenotypes are now included in the Target Of section on gene pages.

The gene pages also now display protein modification data from two large-scale datasets:

  • Wilson-Grady JT, VillĂ©n J, Gygi SP. 2008 .Phosphoproteome analysis of fission yeast. J Proteome Res. 2008 Mar;7(3):1088-97. doi:10.1021/pr7006335. PMID:18257517
  • Carpy A, Krug K, Graf S, Koch A, Popic S, Hauf...
Monday, 30th Jun, 2014

PomBase was an early adopter of annotation extensions, which add spatial, temporal, or substrate/target details to GO annotations. The GO Consortium has now published a paper describing its implementation of annotation extensions, in which PomBase examples and its gene page display figure prominently:

Huntley, R.P. et al. (2014) A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics 2014, 15:155. doi:10.1186/1471-2105-15-155 PMID:24885854