Dear pombe researchers,
We have updated the data available on the PomBase web site. The data now represents manual curation through October 27, 2014, including 225 community-curated publications.
The Phenotype section of the gene pages now includes data from the high-throughput microscopy analysis of viable deletion mutants reported in:
Graml V, Studera X, Lawson JL, Chessel A, Geymonat M, Bortfeld-Miller M, Walter T, Wagstaff L, Piddini E, Carazo-Salas RE. 2014. A Genomic Multiprocess Survey of Machineries that Control and Link Cell Shape, Microtubule Organization, and Cell-Cycle Progression. Dev Cell. 2014 Oct 27;31(2):227-39. http://europepmc.org/abstract/MED/25373780
Links to the accompanying SYSGRO resource have also been added to the External References section of the gene pages.
In the genome browser, we have added tracks for intron branch point data from:
Bitton DA, Rallis C, Jeffares DC, Smith GC, Chen YY, Codlin S, Marguerat S, BÃ¤hlre J. 2014. LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq. Genome Res. 2014 Jul;24(7):1169-79. http://europepmc.org/abstract/MED/24709818
We have greatly improved search results for GO and FYPO annotations: both now follow more relationship types within the ontology to retrieve genes annotated to a term. The PomBase GO search now includes the "regulates" relationships, so its search results are consistent with those in the GO Consortium's AmiGO browser. For example, a search for "cytokinesis" will include genes annotated to "regulation of cytokinesis" in both AmiGO and PomBase.
The FYPO search now uses "has_part", "has_output", and "output_of" as well as "is_a" and "part_of". For example, FYPO includes the relation inviable swollen elongated cell with enlarged nucleus (FYPO:0002083) has_part swollen cell (FYPO:0000025). Genes annotated to FYPO:0002083 will therefore be retrieved in a search for FYPO:0000025.
You can find more information on ontology relations and annotation propagation in the PomBase GO documentation, advanced search documentation, and pages linked there.
We have also made a few other adjustments to the PomBase pages. Notably, the gene page Phenotype section now includes a highlighted sub-header that indicates whether a deletion mutant is viable or inviable (or if viability depends on conditions).
In the Downloads section, a file of protein complex subunits is now available, and other files have been updated.
As usual, please don't hesitate to alert us of any other problems with data or site performance, or if you have any questions.
The PomBase Staff