Between 2007-12-10 and 2007-12-13, the sequence of Chromosome VII was updated, affecting features EFG1/YGR271C-A and YGR272C; and the annotations of the mating-type loci (HML, MAT, HMR) on Chromosome III were updated.
has
been added to references that are associated with curated genomics
data sets at the Yeast Functional Genomics Database (YFGdb).
YFGdb is an ongoing project to collect, curate, and disseminate all yeast functional genomics
data by providing a means to view and download the data. Currently, there are links from over 450 papers in SGD to the
corresponding YFGdb page. View references curated to the literature topic Genomic
expression study for examples.
Links to the Fungal Orthogroups Repository have been added to the "Comparison Resources" pulldown menu on the Locus Summary pages of 5,780 protein-coding genes. The Fungal Orthogroups Repository is a database of orthology groups among protein-coding genes of 17 Ascomycete fungi, maintained by the Regev group at the Broad Institute, MIT. Orthology groups were determined by the SYNERGY method, as described in the publication Wapinski et al., 2007.
Links to the SPELL (Serial Pattern of Expression Levels Locator) resource have been added to the "Functional Analysis" pulldown menu on the Locus Summary pages of all open reading frames. SPELL searches large gene expression microarray compendia to identify datasets relevant to a gene or set of genes, and then identifies genes in those datasets whose expression is similar to that of the query set. SPELL is described in Hibbs et al., 2007.
Annotations assigned from published literature (Manually curated and High-throughput) will continue to be the primary set of GO annotations for S. cerevisiae gene products. Computational annotations are not queried by the GO Term Finder and GO Slim Mapper tools, nor are they included in SGD's gene_association.sgd file containing GO annotations for S. cerevisiae gene products.
Between 2007-09-04 and 2007-09-07, annotations were updated for 3 ORFs: MSH3/YCR092C, YKR005C, and LSM7/YNL147W.
Between 2007-07-09 and 2007-07-13, intron annotations were updated for 9 ORFs: HPC2/YBR215W, IWR1/YDL115C, GIM4/YEL003W, PTC7/YHR076W, CGI121/YML036W, RPL20A/YMR242C, HRB1/YNL004W, RPL20B/YOR312C, and YPR153W.
In addition, the list of Uncharacterized ORFs analyzed in this recent publication is available from the same location of the FTP site. SGD staff have reviewed the status of the 126 named genes mentioned in the paper and have upgraded over half of them to Verified status based on recent publications. A current list of Uncharacterized ORFs can be retrieved via SGD's Genome Snapshot or Advanced Search.
SGD classifies ORFs as Verified, Uncharacterized, and Dubious according to the degree of certainty that each ORF encodes a functional protein. SGD considers these classifications a working hypothesis, and the designations change based on published experimental results.
Between 2007-05-07 and 2007-05-11, annotation updates were made affecting 10 RNA features (snR3, snR18, snR30, snR34, snR35, snR36, snR46, snR70, snR78, and HRA1) and one new ORF was added (YPR010C-A).
Between 2007-04-02 and 2007-04-06, annotation updates were made affecting features snR47 and YFR045W, sequence updates were made affecting features SSA1/YAL005C and YAL004W, and LTR annotations were updated on Chromosomes II, III, IV, V, IX, X, and XII.
Between 2007-03-06 and 2007-03-09, ARS element annotations were
updated on Chromosomes
I,
III,
IV,
and
VI.
Between 2007-02-06 and 2007-02-07, annotation updates were made
affecting features HRA1
and YRF1-8/YOR396W,
and two new ARS elements (ARS1200-1,
ARS1200-2)
were added.